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/7775246/working' mkdir: created directory `/scratch/stefan/7775246/working/protonate' Storing results in /scratch/stefan/7775246/finished Working in /scratch/stefan/7775246/working /scratch/stefan/7775246/working /scratch/stefan/7775246 /scratch/stefan/7775246/working/protonate /scratch/stefan/7775246/working /scratch/stefan/7775246 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1012 protomers created Coalesing and merging protomers 1006 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1006 protomers after new stereo-center expansion /scratch/stefan/7775246/working /scratch/stefan/7775246 Bulk generating 3D conformations all protomers in /scratch/stefan/7775246/working/3D mkdir: created directory `/scratch/stefan/7775246/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7775246/working/protonate/xaaabji-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' 1007 3D conformations generated for 1000 compounds Building REAL300004918001 mkdir: created directory `/scratch/stefan/7775246/working/building' mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918001' /scratch/stefan/7775246/working/building/REAL300004918001 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918001 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918001/0 /scratch/stefan/7775246/working/building/REAL300004918001 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1 `/scratch/stefan/7775246/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004918001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918001 none CC#CCC(NC(=O)CC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 84, 27, 27, 8, 27, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 84, 119, 119, 194, 194, 194, 194, 194, 84, 27, 8, 8, 1, 4, 4, 3, 4, 4, 1] 201 rigid atoms, others: [32, 38, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 937 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918001 none CC#CCC(NC(=O)CC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 92, 35, 35, 16, 35, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 92, 125, 125, 201, 201, 201, 201, 201, 92, 35, 16, 16, 4, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38]) total number of confs: 946 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918001 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918001 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `/scratch/stefan/7775246/finished' Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918001/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918001 Building REAL300004918002 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918002' /scratch/stefan/7775246/working/building/REAL300004918002 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918002 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918002/0 /scratch/stefan/7775246/working/building/REAL300004918002 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/2 `/scratch/stefan/7775246/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)OC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918002 none CC#CCC(NC(=O)CC1=C(C)OC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 199, 199, 88, 43, 43, 8, 43, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 88, 125, 125, 199, 199, 199, 199, 199, 88, 43, 8, 8, 2, 2, 2, 3, 3, 1, 3, 3] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 972 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918002 none CC#CCC(NC(=O)CC1=C(C)OC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 69, 69, 19, 69, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 117, 150, 150, 201, 201, 201, 201, 201, 117, 69, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 965 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918002 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918002 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918002/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918002 Building REAL300004918003 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918003' /scratch/stefan/7775246/working/building/REAL300004918003 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918003 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918003/0 /scratch/stefan/7775246/working/building/REAL300004918003 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/3 `/scratch/stefan/7775246/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C(F)(F)F)=C2)N=C1)C(=O)[O-]) `REAL300004918003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918003 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C(F)(F)F)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 3, 6, 6, 6, 6, 6, 6, 1, 1, 34, 51, 51, 67, 67, 67, 67, 67, 34, 13, 2, 2, 2, 6, 6, 6, 6, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 362 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918003 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C(F)(F)F)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 49, 49, 6, 49, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 6, 119, 148, 148, 201, 201, 201, 201, 201, 119, 49, 6, 6, 6, 1, 1, 1, 1, 6] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 951 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918003 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918003 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918003/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918003 Building REAL300004918004 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918004' /scratch/stefan/7775246/working/building/REAL300004918004 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918004 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918004/0 /scratch/stefan/7775246/working/building/REAL300004918004 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/4 `/scratch/stefan/7775246/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SCC2=CSC(C)=N2)C=C1)C(=O)[O-]) `REAL300004918004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918004 none CC#CCC(NC(=O)C1=CC=C(SCC2=CSC(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 1, 14, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 29, 51, 51, 51, 51, 51, 1, 1, 7, 11, 11, 21, 21, 21, 21, 21, 7, 3, 1, 1, 29, 29, 51, 52, 52, 52, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 40, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 235 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918004 none CC#CCC(NC(=O)C1=CC=C(SCC2=CSC(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 1, 14, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 81, 81, 50, 81, 32, 51, 51, 16, 6, 1, 1, 1, 1, 1, 1, 1, 51, 51, 110, 137, 137, 201, 201, 201, 201, 201, 110, 81, 52, 52, 6, 6, 1, 2, 2, 2, 51, 51] 201 rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 993 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918004 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918004 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918004/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918004 Building REAL300004918005 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918005' /scratch/stefan/7775246/working/building/REAL300004918005 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918005 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918005/0 /scratch/stefan/7775246/working/building/REAL300004918005 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/5 `/scratch/stefan/7775246/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC=CCC1C1=NC2=CC=CC=C2S1)C(=O)[O-]) `REAL300004918005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918005 none CC#CCC(NC(=O)C1CC=CCC1C1=NC2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 9, 10, 10, 10, 20, 34, 34, 54, 54, 54, 54, 54, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 9, 10] 125 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918005 none CC#CCC(NC(=O)C1CC=CCC1C1=NC2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 76, 38, 38, 10, 38, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 100, 100, 125, 125, 125, 125, 125, 76, 38, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 125 rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 620 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918005 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918005 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918005/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918005 Building REAL300004918006 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918006' /scratch/stefan/7775246/working/building/REAL300004918006 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918006 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918006/0 /scratch/stefan/7775246/working/building/REAL300004918006 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/6 `/scratch/stefan/7775246/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=N1)C(=O)[O-]) `REAL300004918006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918006 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 19, 7, 7, 1, 7, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 1, 19, 30, 30, 53, 53, 53, 53, 53, 19, 7, 1, 9, 9, 19, 19, 19, 19, 19] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918006 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 62, 62, 19, 62, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 118, 155, 155, 201, 201, 201, 201, 201, 118, 62, 19, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 948 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918006 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918006 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918006/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918006 Building REAL300004918007 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918007' /scratch/stefan/7775246/working/building/REAL300004918007 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918007 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918007/0 /scratch/stefan/7775246/working/building/REAL300004918007 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/7 `/scratch/stefan/7775246/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC(=O)NC1CCCCC1)C(=O)[O-]) `REAL300004918007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918007 none CC#CCC(NC(=O)CCCNC(=O)NC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 35, 34, 34, 23, 34, 23, 22, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 45, 45, 45, 45, 45, 35, 34, 23, 23, 23, 23, 22, 22, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [48, 49, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 47] 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: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918007 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918007 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918007/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918007 Building REAL300004918008 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918008' /scratch/stefan/7775246/working/building/REAL300004918008 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918008 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918008/0 /scratch/stefan/7775246/working/building/REAL300004918008 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/8 `/scratch/stefan/7775246/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=NC(C(F)(F)F)=NN2)C(C)=N1)C(=O)[O-]) `REAL300004918008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918008 none CC#CCC(NC(=O)C1=NN(C2=NC(C(F)(F)F)=NN2)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 1, 5, 15, 15, 15, 8, 8, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 34, 12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 3, 3, 1, 1, 1, 34, 51, 51, 76, 76, 76, 76, 76, 34, 12, 3, 2, 2, 2] 88 rigid atoms, others: [6, 8, 9, 10, 11, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918008 none CC#CCC(NC(=O)C1=NN(C2=NC(C(F)(F)F)=NN2)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 1, 5, 15, 15, 15, 8, 8, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 53, 22, 22, 3, 22, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 53, 69, 69, 88, 88, 88, 88, 88, 53, 22, 1, 4, 4, 4] 88 rigid atoms, others: [33, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918008 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918008 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918008/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918008 Building REAL300004918009 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918009' /scratch/stefan/7775246/working/building/REAL300004918009 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918009 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918009/0 /scratch/stefan/7775246/working/building/REAL300004918009 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/9 `/scratch/stefan/7775246/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OC(F)F)C=C1)C(=O)[O-]) `REAL300004918009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918009 none CC#CCC(NC(=O)CCC1=CC=C(OC(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 1, 1, 24, 40, 40, 53, 53, 53, 53, 53, 24, 9, 1, 1, 1, 1, 1, 1, 30, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 37, 6, 8, 9, 10, 11, 12, 13, 14, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918009 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918009 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918009/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918009 Building REAL300004918010 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918010' /scratch/stefan/7775246/working/building/REAL300004918010 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918010 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918010/0 /scratch/stefan/7775246/working/building/REAL300004918010 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/10 `/scratch/stefan/7775246/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2NC3=C(CCCC3)C2=CC=C1)C(=O)[O-]) `REAL300004918010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918010 none CC#CCC(NC(=O)C1=C2NC3=C(CCCC3)C2=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 42, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 62, 62, 99, 99, 99, 99, 99, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918010 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918010 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918010/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918010 Building REAL300004918011 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918011' /scratch/stefan/7775246/working/building/REAL300004918011 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918011 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918011/0 /scratch/stefan/7775246/working/building/REAL300004918011 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/11 `/scratch/stefan/7775246/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OC)C(Br)=C1)C(=O)[O-]) `REAL300004918011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918011 none CC#CCC(NC(=O)CCC1=CC=C(OC)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 87, 25, 25, 6, 24, 2, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 88, 131, 131, 158, 158, 158, 158, 158, 88, 25, 6, 6, 2, 2, 1, 1, 4, 4, 4, 1] 201 rigid atoms, others: [33, 34, 38, 9, 10, 11, 12, 13, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918011 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918011 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918011/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918011 Building REAL300004918012 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918012' /scratch/stefan/7775246/working/building/REAL300004918012 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004918012 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918012/0 /scratch/stefan/7775246/working/building/REAL300004918012 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/12 `/scratch/stefan/7775246/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=C([N+](=O)[O-])C=CC2=NN1)C(=O)[O-]) `REAL300004918012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918012 none CC#CCC(NC(=O)C1=C2C=C([N+](=O)[O-])C=CC2=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 61, 61, 100, 100, 100, 100, 100, 45, 13, 1, 1, 1, 1] 100 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 448 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918012 /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `1' /scratch/stefan/7775246/working/building/REAL300004918012/1 /scratch/stefan/7775246/working/building/REAL300004918012 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/13 `/scratch/stefan/7775246/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NNC2=CC=C([N+](=O)[O-])C=C21)C(=O)[O-]) `REAL300004918012.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004918012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918012 none CC#CCC(NC(=O)C1=NNC2=CC=C([N+](=O)[O-])C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 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, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 41, 41, 57, 57, 57, 57, 57, 28, 10, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918012 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918012 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918012/0.* 1: /scratch/stefan/7775246/working/building/REAL300004918012/1.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918012 Building REAL300004918013 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918013' /scratch/stefan/7775246/working/building/REAL300004918013 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918013 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918013/0 /scratch/stefan/7775246/working/building/REAL300004918013 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/14 `/scratch/stefan/7775246/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004918013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918013 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 36, 52, 52, 77, 77, 77, 77, 77, 36, 13, 1, 4, 4, 2, 4, 4] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918013 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 55, 30, 30, 4, 30, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 55, 64, 64, 79, 79, 79, 79, 79, 55, 30, 4, 1, 1, 1, 1, 1] 79 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918013 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918013 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918013/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918013 Building REAL300004918014 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918014' /scratch/stefan/7775246/working/building/REAL300004918014 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918014 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918014/0 /scratch/stefan/7775246/working/building/REAL300004918014 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/15 `/scratch/stefan/7775246/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-]) `REAL300004918014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918014 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 1, 32, 42, 42, 61, 61, 61, 61, 61, 32, 12, 2, 2, 2, 5, 5, 5, 5, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 300 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918014 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 48, 48, 5, 48, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 105, 143, 143, 201, 201, 201, 201, 201, 105, 48, 5, 5, 5, 1, 1, 1, 1, 5] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 981 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918014 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918014 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918014/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918014 Building REAL300004918015 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918015' /scratch/stefan/7775246/working/building/REAL300004918015 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918015 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918015/0 /scratch/stefan/7775246/working/building/REAL300004918015 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/16 `/scratch/stefan/7775246/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=CC=C1[N-]S(C)(=O)=O)C(=O)[O-]) `REAL300004918015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918015 none CC#CCC(NC(=O)C1=CC(C)=CC=C1[N-]S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 4, 3, 1, 2, 2, 2, 1, 1, 3, 3, 3] 9 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918015 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918015 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918015/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918015 Building REAL300004918016 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918016' /scratch/stefan/7775246/working/building/REAL300004918016 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918016 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918016/0 /scratch/stefan/7775246/working/building/REAL300004918016 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/17 `/scratch/stefan/7775246/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(S(N)(=O)=O)S1)C(=O)[O-]) `REAL300004918016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918016 none CC#CCC(NC(=O)CC1=CC=C(S(N)(=O)=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 8, 11, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 48, 25, 25, 8, 25, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 48, 76, 76, 106, 106, 106, 106, 106, 48, 25, 8, 8, 1, 1, 5, 5] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918016 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918016 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918016/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918016 Building REAL300004918017 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918017' /scratch/stefan/7775246/working/building/REAL300004918017 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918017 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918017/0 /scratch/stefan/7775246/working/building/REAL300004918017 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/18 `/scratch/stefan/7775246/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCC(C(F)(F)F)C1)C(=O)[O-]) `REAL300004918017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918017 none CC#CCC(NC(=O)C1CCCC(C(F)(F)F)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 46, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 46, 67, 67, 103, 103, 103, 103, 103, 46, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918017 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918017 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918017/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918017 Building REAL300004918018 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918018' /scratch/stefan/7775246/working/building/REAL300004918018 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918018 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918018/0 /scratch/stefan/7775246/working/building/REAL300004918018 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/19 `/scratch/stefan/7775246/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COCCOC1=CC=CC=C1)C(=O)[O-]) `REAL300004918018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918018 none CC#CCC(NC(=O)COCCOC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 180, 159, 159, 119, 159, 54, 22, 10, 3, 1, 1, 1, 1, 1, 1, 1, 180, 190, 190, 201, 201, 201, 201, 201, 180, 158, 119, 119, 22, 22, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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: 838 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918018 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918018 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918018/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918018 Building REAL300004918019 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918019' /scratch/stefan/7775246/working/building/REAL300004918019 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918019 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918019/0 /scratch/stefan/7775246/working/building/REAL300004918019 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/20 `/scratch/stefan/7775246/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COCC1=CC=CC(OC)=C1)C(=O)[O-]) `REAL300004918019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918019 none CC#CCC(NC(=O)COCC1=CC=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 181, 150, 150, 91, 150, 28, 8, 1, 1, 1, 1, 1, 1, 1, 3, 1, 181, 184, 184, 193, 193, 193, 193, 193, 181, 150, 91, 91, 8, 8, 1, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [33, 34, 35, 39, 10, 11, 12, 13, 14, 15, 16, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918019 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918019 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918019/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918019 Building REAL300004918020 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918020' /scratch/stefan/7775246/working/building/REAL300004918020 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918020 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918020/0 /scratch/stefan/7775246/working/building/REAL300004918020 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/21 `/scratch/stefan/7775246/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OCC1=CC=CC(OC)=C1)C(=O)[O-]) `REAL300004918020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918020 none CC#CCC(NC(=O)C(C)OCC1=CC=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 152, 102, 102, 60, 102, 30, 60, 8, 1, 1, 1, 1, 1, 1, 1, 3, 1, 152, 156, 156, 196, 196, 196, 196, 196, 152, 102, 60, 60, 60, 60, 8, 8, 1, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [36, 37, 38, 42, 11, 12, 13, 14, 15, 16, 17, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 895 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918020 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918020 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918020/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918020 Building REAL300004918021 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918021' /scratch/stefan/7775246/working/building/REAL300004918021 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918021 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918021/0 /scratch/stefan/7775246/working/building/REAL300004918021 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/22 `/scratch/stefan/7775246/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OCC)C=C1)C(=O)[O-]) `REAL300004918021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918021 none CC#CCC(NC(=O)CCC1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 46, 19, 19, 5, 19, 3, 1, 1, 1, 1, 1, 1, 6, 15, 1, 1, 46, 69, 69, 117, 117, 117, 117, 117, 46, 19, 5, 5, 3, 3, 1, 1, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [33, 34, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 605 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918021 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918021 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918021/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918021 Building REAL300004918022 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918022' /scratch/stefan/7775246/working/building/REAL300004918022 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918022 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918022/0 /scratch/stefan/7775246/working/building/REAL300004918022 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/23 `/scratch/stefan/7775246/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCCNC(=O)NC1CCCCC1)C(=O)[O-]) `REAL300004918022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918022 none CC#CCC(NC(=O)CCCCCNC(=O)NC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 106, 67, 67, 28, 67, 20, 28, 20, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 106, 141, 141, 197, 197, 197, 197, 197, 106, 67, 30, 30, 28, 28, 28, 28, 28, 28, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 50, 54, 51, 49, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 55, 52, 53] 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: 1117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918022 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918022 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918022/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918022 Building REAL300004918023 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918023' /scratch/stefan/7775246/working/building/REAL300004918023 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918023 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918023/0 /scratch/stefan/7775246/working/building/REAL300004918023 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/24 `/scratch/stefan/7775246/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CCC)CC1CCCCC1)C(=O)[O-]) `REAL300004918023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918023 none CC#CCC(NC(=O)C(CCC)CC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 69, 28, 28, 8, 28, 5, 8, 19, 23, 1, 1, 1, 1, 1, 1, 1, 69, 100, 100, 150, 150, 150, 150, 150, 69, 28, 8, 19, 19, 23, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 45, 49, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 811 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918023 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918023 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918023/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918023 Building REAL300004918024 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918024' /scratch/stefan/7775246/working/building/REAL300004918024 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918024 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918024/0 /scratch/stefan/7775246/working/building/REAL300004918024 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/25 `/scratch/stefan/7775246/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC(C2=CC=C(F)C=C2)=N1)C(=O)[O-]) `REAL300004918024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918024 none CC#CCC(NC(=O)CC1=COC(C2=CC=C(F)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 93, 43, 43, 7, 43, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 93, 138, 138, 197, 197, 197, 197, 197, 93, 43, 7, 7, 1, 4, 4, 4, 4] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 1008 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918024 none CC#CCC(NC(=O)CC1=COC(C2=CC=C(F)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 74, 74, 16, 74, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 120, 157, 157, 201, 201, 201, 201, 201, 120, 74, 16, 16, 4, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 992 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918024 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918024 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918024/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918024 Building REAL300004918025 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918025' /scratch/stefan/7775246/working/building/REAL300004918025 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918025 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918025/0 /scratch/stefan/7775246/working/building/REAL300004918025 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/26 `/scratch/stefan/7775246/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(COC2=CC=CC(F)=C2)=C1)C(=O)[O-]) `REAL300004918025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918025 none CC#CCC(NC(=O)C1=CC=CC(COC2=CC=CC(F)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 1, 12, 17, 17, 23, 23, 23, 23, 23, 12, 5, 1, 1, 1, 9, 9, 16, 16, 16, 16, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918025 none CC#CCC(NC(=O)C1=CC=CC(COC2=CC=CC(F)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 57, 57, 16, 57, 16, 15, 16, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 16, 103, 146, 146, 201, 201, 201, 201, 201, 103, 57, 15, 16, 16, 2, 2, 1, 1, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 1018 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918025 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918025 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918025/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918025 Building REAL300004918026 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918026' /scratch/stefan/7775246/working/building/REAL300004918026 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918026 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918026/0 /scratch/stefan/7775246/working/building/REAL300004918026 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/27 `/scratch/stefan/7775246/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(OC(F)F)C=C(C)S1)C(=O)[O-]) `REAL300004918026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918026 none CC#CCC(NC(=O)C1=C(OC(F)F)C=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 15, 15, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 1, 5, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 6, 1, 2, 2, 2] 8 rigid atoms, others: [6, 8, 9, 10, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918026 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918026 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918026/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918026 Building REAL300004918027 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918027' /scratch/stefan/7775246/working/building/REAL300004918027 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918027 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918027/0 /scratch/stefan/7775246/working/building/REAL300004918027 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/28 `/scratch/stefan/7775246/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2C)C(F)=C1)C(=O)[O-]) `REAL300004918027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918027 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2C)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 1, 1, 1, 27, 42, 42, 81, 81, 81, 81, 81, 27, 7, 1, 1, 7, 7, 7, 7, 7, 7, 1] 179 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918027 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2C)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 92, 29, 29, 6, 29, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 92, 118, 118, 179, 179, 179, 179, 179, 92, 29, 7, 7, 1, 1, 1, 2, 2, 2, 7] 179 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918027 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918027 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918027/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918027 Building REAL300004918028 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918028' /scratch/stefan/7775246/working/building/REAL300004918028 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918028 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918028/0 /scratch/stefan/7775246/working/building/REAL300004918028 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/29 `/scratch/stefan/7775246/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1SCCC2=CC=CC=C21)C(=O)[O-]) `REAL300004918028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918028 none CC#CCC(NC(=O)C1SCCC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 32, 32, 59, 59, 59, 59, 59, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918028 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918028 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918028/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918028 Building REAL300004918029 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918029' /scratch/stefan/7775246/working/building/REAL300004918029 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918029 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918029/0 /scratch/stefan/7775246/working/building/REAL300004918029 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/30 `/scratch/stefan/7775246/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(C(F)(F)F)=CC=C2N1C)C(=O)[O-]) `REAL300004918029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918029 none CC#CCC(NC(=O)C1=CC2=CC(C(F)(F)F)=CC=C2N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 41, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 41, 52, 52, 67, 67, 67, 67, 67, 41, 13, 1, 1, 1, 1, 2, 2, 2] 67 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 329 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918029 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918029 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918029/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918029 Building REAL300004918030 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918030' /scratch/stefan/7775246/working/building/REAL300004918030 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918030 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918030/0 /scratch/stefan/7775246/working/building/REAL300004918030 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/31 `/scratch/stefan/7775246/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC2=NOC(CC)=N2)C=C1)C(=O)[O-]) `REAL300004918030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918030 none CC#CCC(NC(=O)C1=CC=C(OCC2=NOC(CC)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 12, 1, 5, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 64, 17, 1, 1, 7, 11, 11, 18, 18, 18, 18, 18, 7, 3, 1, 1, 2, 2, 64, 64, 64, 64, 64, 1, 1] 201 rigid atoms, others: [33, 34, 43, 6, 8, 9, 10, 11, 12, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918030 none CC#CCC(NC(=O)C1=CC=C(OCC2=NOC(CC)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 12, 1, 5, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 68, 33, 33, 17, 33, 9, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 7, 1, 17, 17, 68, 103, 103, 132, 132, 132, 132, 132, 68, 33, 17, 17, 9, 9, 7, 7, 8, 8, 8, 17, 17] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918030 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918030 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918030/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918030 Building REAL300004918031 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918031' /scratch/stefan/7775246/working/building/REAL300004918031 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918031 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918031/0 /scratch/stefan/7775246/working/building/REAL300004918031 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/32 `/scratch/stefan/7775246/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(C)C=C(F)C=C2N1)C(=O)[O-]) `REAL300004918031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918031 none CC#CCC(NC(=O)C1=CC2=C(C)C=C(F)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 15, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 72, 72, 72, 72, 72, 39, 12, 1, 2, 2, 2, 1, 1, 1] 72 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918031 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918031 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918031/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918031 Building REAL300004918032 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918032' /scratch/stefan/7775246/working/building/REAL300004918032 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918032 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918032/0 /scratch/stefan/7775246/working/building/REAL300004918032 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/33 `/scratch/stefan/7775246/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)NC1=C([N+](=O)[O-])C(C)=NN1C)C(=O)[O-]) `REAL300004918032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918032 none CC#CCC(NC(=O)C(CC)NC1=C([N+](=O)[O-])C(C)=NN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 11, 11, 1, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [96, 96, 96, 48, 20, 20, 6, 20, 3, 6, 10, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 48, 68, 68, 96, 96, 96, 96, 96, 48, 20, 6, 10, 10, 10, 10, 10, 3, 2, 2, 2, 2, 2, 2] 99 rigid atoms, others: [11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 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: 519 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918032 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918032 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918032/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918032 Building REAL300004918033 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918033' /scratch/stefan/7775246/working/building/REAL300004918033 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918033 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918033/0 /scratch/stefan/7775246/working/building/REAL300004918033 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/34 `/scratch/stefan/7775246/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CN(C)N=C2)S1)C(=O)[O-]) `REAL300004918033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918033 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CN(C)N=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 8, 5, 8, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 41, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 4, 5, 4, 5, 1, 41, 61, 61, 94, 94, 94, 94, 94, 41, 12, 2, 2, 2, 5, 5, 5, 5, 5] 140 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 466 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918033 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CN(C)N=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 8, 5, 8, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 85, 34, 34, 4, 34, 4, 4, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 85, 106, 106, 140, 140, 140, 140, 140, 85, 34, 5, 5, 5, 1, 2, 2, 2, 1] 140 rigid atoms, others: [33, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 665 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918033 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918033 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918033/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918033 Building REAL300004918034 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918034' /scratch/stefan/7775246/working/building/REAL300004918034 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918034 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918034/0 /scratch/stefan/7775246/working/building/REAL300004918034 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/35 `/scratch/stefan/7775246/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004918034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918034 none CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 2, 9, 9, 9, 37, 61, 61, 89, 89, 89, 89, 89, 37, 11, 1, 1, 1, 2, 2, 2, 1, 9, 9, 8, 9] 201 rigid atoms, others: [32, 33, 34, 38, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 483 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918034 none CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 55, 55, 9, 55, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 130, 158, 158, 201, 201, 201, 201, 201, 130, 55, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 920 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918034 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918034 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918034/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918034 Building REAL300004918035 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918035' /scratch/stefan/7775246/working/building/REAL300004918035 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918035 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918035/0 /scratch/stefan/7775246/working/building/REAL300004918035 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/36 `/scratch/stefan/7775246/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC2=NC=CS2)=C1)C(=O)[O-]) `REAL300004918035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918035 none CC#CCC(NC(=O)C1=CC=CC(OC2=NC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 1, 13, 19, 19, 32, 32, 32, 32, 32, 13, 5, 1, 1, 1, 16, 16, 1] 201 rigid atoms, others: [32, 35, 6, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918035 none CC#CCC(NC(=O)C1=CC=CC(OC2=NC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 97, 49, 49, 16, 49, 16, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 16, 97, 134, 134, 201, 201, 201, 201, 201, 97, 49, 16, 16, 16, 1, 1, 16] 201 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 951 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918035 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918035 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918035/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918035 Building REAL300004918036 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918036' /scratch/stefan/7775246/working/building/REAL300004918036 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918036 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918036/0 /scratch/stefan/7775246/working/building/REAL300004918036 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/37 `/scratch/stefan/7775246/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)CC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918036 none CC#CCC(NC(=O)C(CC)CC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 85, 37, 37, 9, 37, 3, 9, 15, 1, 1, 1, 1, 1, 1, 1, 1, 85, 121, 121, 184, 184, 184, 184, 184, 85, 37, 9, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 937 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918036 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918036 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918036/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918036 Building REAL300004918037 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918037' /scratch/stefan/7775246/working/building/REAL300004918037 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918037 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918037/0 /scratch/stefan/7775246/working/building/REAL300004918037 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/38 `/scratch/stefan/7775246/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CSC(Br)=C1)C(=O)[O-]) `REAL300004918037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918037 none CC#CCC(NC(=O)C=CC1=CSC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 106, 50, 50, 6, 50, 6, 1, 1, 1, 1, 1, 1, 1, 106, 134, 134, 179, 179, 179, 179, 179, 106, 50, 7, 6, 1, 1] 179 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 821 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918037 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918037 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918037/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918037 Building REAL300004918038 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918038' /scratch/stefan/7775246/working/building/REAL300004918038 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918038 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918038/0 /scratch/stefan/7775246/working/building/REAL300004918038 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/39 `/scratch/stefan/7775246/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC1CCC1)C(=O)[O-]) `REAL300004918038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918038 none CC#CCC(NC(=O)C1=CC=CC=C1OC1CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 32, 52, 52, 99, 99, 99, 99, 99, 32, 12, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 524 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918038 none CC#CCC(NC(=O)C1=CC=CC=C1OC1CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 79, 79, 25, 79, 25, 25, 22, 25, 25, 7, 1, 1, 1, 1, 1, 119, 152, 152, 201, 201, 201, 201, 201, 119, 79, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 914 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918038 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918038 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918038/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918038 Building REAL300004918039 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918039' /scratch/stefan/7775246/working/building/REAL300004918039 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918039 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918039/0 /scratch/stefan/7775246/working/building/REAL300004918039 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/40 `/scratch/stefan/7775246/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=C(F)C=CC=C1F)C(=O)[O-]) `REAL300004918039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918039 none CC#CCC(NC(=O)C1CC1C1=C(F)C=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 24, 9, 9, 1, 9, 1, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 36, 36, 64, 64, 64, 64, 64, 24, 9, 1, 1, 1, 1, 3, 2, 3] 74 rigid atoms, others: [32, 6, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918039 none CC#CCC(NC(=O)C1CC1C1=C(F)C=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 33, 14, 14, 3, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 46, 46, 74, 74, 74, 74, 74, 33, 14, 3, 3, 3, 3, 1, 1, 1] 74 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918039 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918039 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918039/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918039 Building REAL300004918040 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918040' /scratch/stefan/7775246/working/building/REAL300004918040 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918040 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918040/0 /scratch/stefan/7775246/working/building/REAL300004918040 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/41 `/scratch/stefan/7775246/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)SC(Br)=C1)C(=O)[O-]) `REAL300004918040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918040 none CC#CCC(NC(=O)C1=C(Br)SC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'Br', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 14, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 25, 38, 38, 68, 68, 68, 68, 68, 25, 7, 1] 68 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918040 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918040 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918040/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918040 Building REAL300004918041 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918041' /scratch/stefan/7775246/working/building/REAL300004918041 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918041 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918041/0 /scratch/stefan/7775246/working/building/REAL300004918041 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/42 `/scratch/stefan/7775246/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)SC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918041 none CC#CCC(NC(=O)C(C)(C)SC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 105, 54, 54, 14, 54, 4, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 105, 142, 142, 201, 201, 201, 201, 201, 105, 54, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 993 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918041 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918041 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918041/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918041 Building REAL300004918042 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918042' /scratch/stefan/7775246/working/building/REAL300004918042 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918042 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918042/0 /scratch/stefan/7775246/working/building/REAL300004918042 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/43 `/scratch/stefan/7775246/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CCC1=CC=CC=C1F)C(=O)[O-]) `REAL300004918042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918042 none CC#CCC(NC(=O)C(C)CCC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 133, 71, 71, 19, 71, 7, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 133, 179, 179, 201, 201, 201, 201, 201, 133, 71, 19, 19, 19, 19, 7, 7, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1074 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918042 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918042 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918042/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918042 Building REAL300004918043 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918043' /scratch/stefan/7775246/working/building/REAL300004918043 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918043 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918043/0 /scratch/stefan/7775246/working/building/REAL300004918043 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/44 `/scratch/stefan/7775246/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(C(C)C)C=C2N1)C(=O)[O-]) `REAL300004918043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918043 none CC#CCC(NC(=O)C1=CC2=CC=C(C(C)C)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 1, 44, 67, 67, 94, 94, 94, 94, 94, 44, 12, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1] 126 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 41, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918043 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918043 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918043/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918043 Building REAL300004918044 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918044' /scratch/stefan/7775246/working/building/REAL300004918044 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918044 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918044/0 /scratch/stefan/7775246/working/building/REAL300004918044 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/45 `/scratch/stefan/7775246/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2CCCCC2=O)C=C1)C(=O)[O-]) `REAL300004918044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918044 none CC#CCC(NC(=O)C1=CC=C(CN2CCCCC2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 1, 1, 9, 16, 16, 35, 35, 35, 35, 35, 9, 3, 1, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918044 none CC#CCC(NC(=O)C1=CC=C(CN2CCCCC2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 39, 39, 8, 39, 7, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 98, 126, 126, 201, 201, 201, 201, 201, 98, 39, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 964 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918044 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918044 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918044/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918044 Building REAL300004918045 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918045' /scratch/stefan/7775246/working/building/REAL300004918045 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918045 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918045/0 /scratch/stefan/7775246/working/building/REAL300004918045 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/46 `/scratch/stefan/7775246/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CCC)N(CC2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004918045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918045 none CC#CCC(NC(=O)C1=C(CCC)N(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 20, 9, 9, 1, 9, 1, 1, 1, 2, 2, 1, 1, 5, 9, 9, 7, 9, 9, 1, 1, 20, 30, 30, 37, 37, 37, 37, 37, 20, 9, 2, 2, 2, 2, 3, 3, 3, 5, 5, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [6, 8, 9, 10, 13, 14, 47, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918045 none CC#CCC(NC(=O)C1=C(CCC)N(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 83, 48, 48, 9, 48, 9, 9, 9, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 83, 109, 109, 133, 133, 133, 133, 133, 83, 48, 15, 15, 15, 15, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46] 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, 47]) total number of confs: 684 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918045 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918045 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918045/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918045 Building REAL300004918046 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918046' /scratch/stefan/7775246/working/building/REAL300004918046 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918046 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918046/0 /scratch/stefan/7775246/working/building/REAL300004918046 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/47 `/scratch/stefan/7775246/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC2=CC=CC=C2NC1=O)C(=O)[O-]) `REAL300004918046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918046 none CC#CCC(NC(=O)CC1=CC2=CC=CC=C2NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 40, 40, 7, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 129, 129, 201, 201, 201, 201, 201, 91, 40, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 967 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918046 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918046 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918046/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918046 Building REAL300004918047 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918047' /scratch/stefan/7775246/working/building/REAL300004918047 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918047 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918047/0 /scratch/stefan/7775246/working/building/REAL300004918047 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/48 `/scratch/stefan/7775246/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC(Cl)=CC(Cl)=C2)S1)C(=O)[O-]) `REAL300004918047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918047 none CC#CCC(NC(=O)C1=CC=C(C2=CC(Cl)=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 2, 7, 7, 7, 1, 40, 63, 63, 94, 94, 94, 94, 94, 40, 12, 1, 1, 7, 2, 7] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918047 none CC#CCC(NC(=O)C1=CC=C(C2=CC(Cl)=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 65, 65, 7, 65, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 133, 157, 157, 201, 201, 201, 201, 201, 133, 65, 7, 7, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 915 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918047 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918047 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918047/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918047 Building REAL300004918048 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918048' /scratch/stefan/7775246/working/building/REAL300004918048 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918048 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918048/0 /scratch/stefan/7775246/working/building/REAL300004918048 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/49 `/scratch/stefan/7775246/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-]) `REAL300004918048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918048 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 31, 42, 42, 57, 57, 57, 57, 57, 31, 10, 2, 2, 2, 6, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918048 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 112, 40, 40, 6, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 112, 151, 151, 201, 201, 201, 201, 201, 112, 40, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 986 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918048 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918048 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918048/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918048 Building REAL300004918049 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918049' /scratch/stefan/7775246/working/building/REAL300004918049 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918049 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918049/0 /scratch/stefan/7775246/working/building/REAL300004918049 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/50 `/scratch/stefan/7775246/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(F)=C2)CCCCC1)C(=O)[O-]) `REAL300004918049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918049 none CC#CCC(NC(=O)C1(C2=CC=CC(F)=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 18, 5, 5, 1, 5, 1, 1, 13, 13, 12, 13, 13, 13, 1, 1, 1, 1, 1, 18, 31, 31, 52, 52, 52, 52, 52, 18, 5, 13, 13, 12, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 42, 43, 44, 16, 17, 18, 19, 20, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918049 none CC#CCC(NC(=O)C1(C2=CC=CC(F)=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 35, 35, 13, 35, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 97, 133, 133, 201, 201, 201, 201, 201, 97, 35, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 995 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918049 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918049 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918049/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918049 Building REAL300004918050 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918050' /scratch/stefan/7775246/working/building/REAL300004918050 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918050 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918050/0 /scratch/stefan/7775246/working/building/REAL300004918050 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/51 `/scratch/stefan/7775246/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=C(F)C=C2)C=CS1)C(=O)[O-]) `REAL300004918050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918050 none CC#CCC(NC(=O)C1=C(C2=CC=C(F)C=C2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 48, 12, 12, 1, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 1, 1, 1, 48, 79, 79, 130, 130, 130, 130, 130, 48, 12, 5, 5, 5, 5, 1, 1] 160 rigid atoms, others: [34, 35, 6, 8, 9, 10, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918050 none CC#CCC(NC(=O)C1=C(C2=CC=C(F)C=C2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 84, 32, 32, 5, 32, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 84, 117, 117, 160, 160, 160, 160, 160, 84, 32, 1, 1, 1, 1, 5, 5] 160 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918050 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918050 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918050/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918050 Building REAL300004918051 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918051' /scratch/stefan/7775246/working/building/REAL300004918051 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918051 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918051/0 /scratch/stefan/7775246/working/building/REAL300004918051 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/52 `/scratch/stefan/7775246/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)NCC(=O)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004918051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918051 none CC#CCC(NC(=O)CCC(=O)NCC(=O)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 39, 35, 35, 35, 35, 35, 35, 35, 35, 29, 7, 1, 7, 1, 1, 1, 1, 1, 2, 1, 1, 39, 39, 39, 70, 70, 70, 70, 70, 39, 35, 35, 35, 35, 35, 35, 29, 29, 1, 1, 2, 2, 2, 1, 1] 70 rigid atoms, others: [41, 42, 14, 47, 16, 17, 18, 19, 20, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918051 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918051 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918051/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918051 Building REAL300004918052 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918052' /scratch/stefan/7775246/working/building/REAL300004918052 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918052 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918052/0 /scratch/stefan/7775246/working/building/REAL300004918052 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/53 `/scratch/stefan/7775246/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C)C(OC)=C2)CCCC1)C(=O)[O-]) `REAL300004918052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918052 none CC#CCC(NC(=O)C1(C2=CC=C(C)C(OC)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 30, 11, 11, 1, 11, 1, 1, 8, 8, 8, 8, 8, 8, 19, 8, 1, 1, 1, 1, 30, 51, 51, 77, 77, 77, 77, 77, 30, 11, 8, 8, 8, 8, 8, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [6, 8, 9, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 411 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918052 none CC#CCC(NC(=O)C1(C2=CC=C(C)C(OC)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 76, 31, 31, 8, 31, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 8, 8, 8, 8, 76, 121, 121, 161, 161, 161, 161, 161, 76, 31, 1, 1, 2, 2, 2, 4, 4, 4, 1, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 17, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 843 number of broken/clashed sets: 156 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918052 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918052 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918052/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918052 Building REAL300004918053 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918053' /scratch/stefan/7775246/working/building/REAL300004918053 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918053 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918053/0 /scratch/stefan/7775246/working/building/REAL300004918053 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/54 `/scratch/stefan/7775246/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(CC(C)(C)CC2=O)NC1=O)C(=O)[O-]) `REAL300004918053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918053 none CC#CCC(NC(=O)C1=CC2=C(CC(C)(C)CC2=O)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 37, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 52, 52, 75, 75, 75, 75, 75, 37, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 75 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918053 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918053 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918053/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918053 Building REAL300004918054 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918054' /scratch/stefan/7775246/working/building/REAL300004918054 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918054 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918054/0 /scratch/stefan/7775246/working/building/REAL300004918054 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/55 `/scratch/stefan/7775246/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)CCC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918054 none CC#CCC(NC(=O)CNC(=O)CCC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 186, 133, 133, 58, 144, 13, 13, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 186, 187, 187, 200, 200, 200, 200, 200, 186, 144, 58, 58, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 44, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918054 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918054 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918054/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918054 Building REAL300004918055 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918055' /scratch/stefan/7775246/working/building/REAL300004918055 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918055 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918055/0 /scratch/stefan/7775246/working/building/REAL300004918055 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/56 `/scratch/stefan/7775246/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(OC)C=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918055 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(OC)C=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 51, 30, 30, 9, 30, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 1, 1, 9, 19, 19, 9, 19, 19, 51, 51, 51, 79, 79, 79, 79, 79, 51, 30, 9, 3, 1, 1, 3, 3, 3, 1, 1, 19, 19, 9, 19, 19] 89 rigid atoms, others: [38, 39, 44, 10, 43, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 418 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918055 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(OC)C=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 31, 16, 16, 4, 16, 1, 4, 10, 10, 10, 19, 19, 10, 10, 31, 19, 19, 1, 1, 1, 1, 1, 1, 31, 31, 31, 57, 57, 57, 57, 57, 31, 16, 4, 10, 19, 19, 31, 31, 31, 19, 19, 1, 1, 1, 1, 1] 89 rigid atoms, others: [8, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 356 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918055 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918055 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918055/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918055 Building REAL300004918056 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918056' /scratch/stefan/7775246/working/building/REAL300004918056 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918056 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918056/0 /scratch/stefan/7775246/working/building/REAL300004918056 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/57 `/scratch/stefan/7775246/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=C(C)C1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918056 none CC#CCC(NC(=O)C=C(C)C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 48, 48, 7, 48, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 115, 147, 147, 201, 201, 201, 201, 201, 115, 48, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 960 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918056 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918056 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918056/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918056 Building REAL300004918057 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918057' /scratch/stefan/7775246/working/building/REAL300004918057 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918057 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918057/0 /scratch/stefan/7775246/working/building/REAL300004918057 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/58 `/scratch/stefan/7775246/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=CC=N2)C(F)=C1)C(=O)[O-]) `REAL300004918057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918057 none CC#CCC(NC(=O)C1=CC=C(N2C=CC=N2)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 29, 43, 43, 81, 81, 81, 81, 81, 29, 7, 1, 1, 8, 7, 8, 1] 133 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918057 none CC#CCC(NC(=O)C1=CC=C(N2C=CC=N2)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 69, 30, 30, 7, 30, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 8, 7, 69, 86, 86, 133, 133, 133, 133, 133, 69, 30, 8, 8, 1, 1, 1, 8] 133 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918057 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918057 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918057/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918057 Building REAL300004918058 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918058' /scratch/stefan/7775246/working/building/REAL300004918058 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918058 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918058/0 /scratch/stefan/7775246/working/building/REAL300004918058 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/59 `/scratch/stefan/7775246/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)C(C)=C(C)N2CCOC)C(=O)[O-]) `REAL300004918058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918058 none CC#CCC(NC(=O)C1=CC=C2C(=C1)C(C)=C(C)N2CCOC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 8, 5, 5, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 23, 17, 29, 29, 58, 58, 58, 58, 58, 17, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 7, 7, 23, 23, 23] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918058 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918058 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918058/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918058 Building REAL300004918059 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918059' /scratch/stefan/7775246/working/building/REAL300004918059 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918059 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918059/0 /scratch/stefan/7775246/working/building/REAL300004918059 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/60 `/scratch/stefan/7775246/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OCC2=CC=CC=C2C)=C1)C(=O)[O-]) `REAL300004918059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918059 none CC#CCC(NC(=O)CC1=CC=CC(OCC2=CC=CC=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 30, 13, 13, 4, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 9, 9, 9, 9, 9, 1, 30, 43, 43, 71, 71, 71, 71, 71, 30, 13, 4, 4, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 48, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918059 none CC#CCC(NC(=O)CC1=CC=CC(OCC2=CC=CC=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 58, 58, 26, 58, 9, 9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 116, 149, 149, 201, 201, 201, 201, 201, 116, 58, 26, 26, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9] 201 rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48]) total number of confs: 1067 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918059 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918059 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918059/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918059 Building REAL300004918060 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918060' /scratch/stefan/7775246/working/building/REAL300004918060 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918060 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918060/0 /scratch/stefan/7775246/working/building/REAL300004918060 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/61 `/scratch/stefan/7775246/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(C)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-]) `REAL300004918060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918060 none CC#CCC(NC(=O)CCC1=C(C)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 55, 18, 19, 2, 18, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 1, 1, 1, 55, 56, 56, 91, 91, 91, 91, 91, 55, 19, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918060 none CC#CCC(NC(=O)CCC1=C(C)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 185, 118, 118, 19, 118, 19, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 185, 186, 186, 201, 201, 201, 201, 201, 185, 118, 19, 19, 19, 19, 11, 11, 11, 5, 5, 1, 1, 2, 2, 2, 1, 1, 11, 11, 11] 201 rigid atoms, others: [50, 49, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918060 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918060 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918060/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918060 Building REAL300004918061 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918061' /scratch/stefan/7775246/working/building/REAL300004918061 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918061 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918061/0 /scratch/stefan/7775246/working/building/REAL300004918061 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/62 `/scratch/stefan/7775246/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(CC)C=C2)C2=C1CCC2)C(=O)[O-]) `REAL300004918061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918061 none CC#CCC(NC(=O)C1=NN(C2=CC=C(CC)C=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 30, 12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 1, 4, 16, 6, 6, 1, 1, 1, 1, 1, 30, 48, 48, 91, 91, 91, 91, 91, 30, 12, 6, 6, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 6, 8, 9, 10, 11, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918061 none CC#CCC(NC(=O)C1=NN(C2=CC=C(CC)C=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 75, 32, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 7, 1, 1, 6, 6, 6, 6, 6, 75, 101, 101, 160, 160, 160, 160, 160, 75, 32, 1, 1, 7, 7, 8, 8, 8, 1, 1, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [34, 35, 41, 10, 11, 12, 13, 14, 15, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918061 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918061 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918061/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918061 Building REAL300004918062 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918062' /scratch/stefan/7775246/working/building/REAL300004918062 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918062 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918062/0 /scratch/stefan/7775246/working/building/REAL300004918062 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/63 `/scratch/stefan/7775246/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(OCC(C)C)C=C2)CCC1)C(=O)[O-]) `REAL300004918062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918062 none CC#CCC(NC(=O)C1(C2=CC=C(OCC(C)C)C=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 19, 9, 9, 1, 9, 1, 1, 2, 2, 1, 1, 7, 11, 19, 19, 2, 2, 1, 1, 1, 19, 34, 34, 57, 57, 57, 57, 57, 19, 9, 2, 2, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [6, 8, 9, 46, 47, 48, 49, 50, 51, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 364 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918062 none CC#CCC(NC(=O)C1(C2=CC=C(OCC(C)C)C=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 19, 9, 9, 2, 9, 1, 1, 1, 1, 1, 1, 6, 10, 19, 19, 1, 1, 2, 2, 2, 19, 34, 34, 57, 57, 57, 57, 57, 19, 9, 1, 1, 10, 10, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 44, 18, 19, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 363 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918062 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918062 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918062/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918062 Building REAL300004918063 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918063' /scratch/stefan/7775246/working/building/REAL300004918063 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918063 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918063/0 /scratch/stefan/7775246/working/building/REAL300004918063 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/64 `/scratch/stefan/7775246/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC(Cl)=C1C)C(=O)[O-]) `REAL300004918063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918063 none CC#CCC(NC(=O)COC1=CC=CC(Cl)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 101, 101, 27, 101, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 178, 178, 201, 201, 201, 201, 201, 141, 101, 27, 27, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 988 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918063 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918063 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918063/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918063 Building REAL300004918064 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918064' /scratch/stefan/7775246/working/building/REAL300004918064 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918064 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918064/0 /scratch/stefan/7775246/working/building/REAL300004918064 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/65 `/scratch/stefan/7775246/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1Br)C(=O)[O-]) `REAL300004918064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918064 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 27, 7, 7, 1, 7, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 1, 27, 43, 43, 83, 83, 83, 83, 83, 27, 7, 4, 4, 4, 4, 1] 83 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918064 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 46, 18, 18, 4, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 46, 60, 60, 83, 83, 83, 83, 83, 46, 18, 1, 1, 1, 1, 4] 83 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918064 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918064 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918064/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918064 Building REAL300004918065 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918065' /scratch/stefan/7775246/working/building/REAL300004918065 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918065 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918065/0 /scratch/stefan/7775246/working/building/REAL300004918065 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/66 `/scratch/stefan/7775246/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NN=CN1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918065 none CC#CCC(NC(=O)CCC1=NN=CN1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 82, 38, 38, 9, 38, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 83, 114, 114, 142, 142, 142, 142, 142, 83, 38, 9, 9, 6, 6, 1, 5, 5, 1, 5, 5] 166 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 759 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918065 none CC#CCC(NC(=O)CCC1=NN=CN1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 133, 79, 79, 22, 79, 15, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 133, 153, 153, 166, 166, 166, 166, 166, 133, 79, 22, 22, 15, 15, 5, 1, 1, 1, 1, 1] 166 rigid atoms, others: [36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 786 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918065 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918065 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918065/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918065 Building REAL300004918066 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918066' /scratch/stefan/7775246/working/building/REAL300004918066 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918066 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918066/0 /scratch/stefan/7775246/working/building/REAL300004918066 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/67 `/scratch/stefan/7775246/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC(F)=CC=C2S1)C(=O)[O-]) `REAL300004918066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918066 none CC#CCC(NC(=O)C1=C(C)C2=CC(F)=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 15, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 46, 46, 66, 66, 66, 66, 66, 33, 9, 2, 2, 2, 1, 1, 1] 66 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918066 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918066 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918066/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918066 Building REAL300004918067 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918067' /scratch/stefan/7775246/working/building/REAL300004918067 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918067 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918067/0 /scratch/stefan/7775246/working/building/REAL300004918067 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/68 `/scratch/stefan/7775246/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC(OC)=CC=C2S1)C(=O)[O-]) `REAL300004918067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918067 none CC#CCC(NC(=O)C1=C(C)C2=CC(OC)=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 40, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 40, 64, 64, 99, 99, 99, 99, 99, 40, 10, 2, 2, 2, 1, 3, 3, 3, 1, 1] 129 rigid atoms, others: [33, 37, 6, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918067 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918067 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918067/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918067 Building REAL300004918068 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918068' /scratch/stefan/7775246/working/building/REAL300004918068 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918068 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918068/0 /scratch/stefan/7775246/working/building/REAL300004918068 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/69 `/scratch/stefan/7775246/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC1=CC(Cl)=CC=C1OC)C(=O)[O-]) `REAL300004918068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918068 none CC#CCC(NC(=O)CCNC1=CC(Cl)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 148, 92, 92, 21, 92, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 150, 188, 188, 179, 179, 179, 179, 179, 150, 92, 21, 21, 15, 15, 3, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 898 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918068 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918068 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918068/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918068 Building REAL300004918069 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918069' /scratch/stefan/7775246/working/building/REAL300004918069 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918069 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918069/0 /scratch/stefan/7775246/working/building/REAL300004918069 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/70 `/scratch/stefan/7775246/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=CC=C(F)C=C2)C1=O)C(=O)[O-]) `REAL300004918069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918069 none CC#CCC(NC(=O)C1CCN(C2=CC=C(F)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 45, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 1, 45, 71, 71, 114, 114, 114, 114, 114, 45, 13, 1, 1, 1, 1, 1, 6, 6, 6, 6] 158 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 546 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918069 none CC#CCC(NC(=O)C1CCN(C2=CC=C(F)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 76, 29, 29, 6, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 76, 107, 107, 158, 158, 158, 158, 158, 76, 29, 6, 6, 6, 6, 6, 1, 1, 1, 1] 158 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 737 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918069 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918069 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918069/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918069 Building REAL300004918070 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918070' /scratch/stefan/7775246/working/building/REAL300004918070 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918070 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918070/0 /scratch/stefan/7775246/working/building/REAL300004918070 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/71 `/scratch/stefan/7775246/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=CC(Cl)=CC=C2Cl)C1=O)C(=O)[O-]) `REAL300004918070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918070 none CC#CCC(NC(=O)C1CCN(C2=CC(Cl)=CC=C2Cl)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 27, 11, 11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 2, 8, 8, 8, 1, 1, 27, 44, 44, 76, 76, 76, 76, 76, 27, 11, 1, 1, 1, 1, 1, 8, 2, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918070 none CC#CCC(NC(=O)C1CCN(C2=CC(Cl)=CC=C2Cl)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 60, 60, 8, 60, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 108, 147, 147, 201, 201, 201, 201, 201, 108, 60, 8, 8, 8, 8, 8, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 985 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918070 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918070 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918070/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918070 Building REAL300004918071 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918071' /scratch/stefan/7775246/working/building/REAL300004918071 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918071 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918071/0 /scratch/stefan/7775246/working/building/REAL300004918071 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/72 `/scratch/stefan/7775246/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=CC=C(Cl)C=C2)C1=O)C(=O)[O-]) `REAL300004918071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918071 none CC#CCC(NC(=O)C1CCN(C2=CC=C(Cl)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 43, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 2, 2, 6, 6, 1, 1, 43, 69, 69, 115, 115, 115, 115, 115, 43, 13, 1, 1, 1, 1, 1, 6, 6, 6, 6] 160 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 554 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918071 none CC#CCC(NC(=O)C1CCN(C2=CC=C(Cl)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 75, 29, 29, 6, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 75, 106, 106, 160, 160, 160, 160, 160, 75, 29, 6, 6, 6, 6, 6, 1, 1, 1, 1] 160 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 752 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918071 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918071 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918071/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918071 Building REAL300004918072 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918072' /scratch/stefan/7775246/working/building/REAL300004918072 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918072 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918072/0 /scratch/stefan/7775246/working/building/REAL300004918072 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/73 `/scratch/stefan/7775246/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]21)C(=O)[O-]) `REAL300004918072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918072 none CC#CCC(NC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 14, 5, 5, 7, 8, 1, 11, 8, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 107, 62, 62, 16, 62, 10, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 148, 148, 201, 201, 201, 201, 201, 107, 62, 16, 16, 10, 10, 8, 8, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1034 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918072 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918072 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918072/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918072 Building REAL300004918073 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918073' /scratch/stefan/7775246/working/building/REAL300004918073 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918073 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918073/0 /scratch/stefan/7775246/working/building/REAL300004918073 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/74 `/scratch/stefan/7775246/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C=C1)C(=O)[O-]) `REAL300004918073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918073 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 36, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 6, 6, 7, 6, 1, 1, 36, 52, 52, 86, 86, 86, 86, 86, 36, 11, 7, 7, 6, 7, 1, 1] 141 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918073 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 83, 41, 41, 7, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 83, 107, 107, 141, 141, 141, 141, 141, 83, 41, 1, 1, 1, 1, 7, 6] 141 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918073 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918073 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918073/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918073 Building REAL300004918074 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918074' /scratch/stefan/7775246/working/building/REAL300004918074 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918074 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918074/0 /scratch/stefan/7775246/working/building/REAL300004918074 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/75 `/scratch/stefan/7775246/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)CC1=CC2=CC=CC=C2C=C1)C(C)C)C(=O)[O-]) `REAL300004918074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918074 none CC#CCC(NC(=O)C(NC(=O)CC1=CC2=CC=CC=C2C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 135, 82, 82, 27, 82, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 59, 53, 135, 170, 170, 180, 180, 180, 180, 180, 135, 82, 27, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59] 201 rigid atoms, others: [45, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918074 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918074 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918074/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918074 Building REAL300004918075 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918075' /scratch/stefan/7775246/working/building/REAL300004918075 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918075 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918075/0 /scratch/stefan/7775246/working/building/REAL300004918075 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/76 `/scratch/stefan/7775246/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=CC2=CC=C(Cl)C=C21)C(=O)[O-]) `REAL300004918075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918075 none CC#CCC(NC(=O)CN1C=CC2=CC=C(Cl)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 45, 45, 8, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 140, 140, 201, 201, 201, 201, 201, 100, 45, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 988 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918075 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918075 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918075/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918075 Building REAL300004918076 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918076' /scratch/stefan/7775246/working/building/REAL300004918076 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918076 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918076/0 /scratch/stefan/7775246/working/building/REAL300004918076 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/77 `/scratch/stefan/7775246/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC2CCCCC2)C=C1)C(=O)[O-]) `REAL300004918076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918076 none CC#CCC(NC(=O)C1=CC=C(OCC2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 40, 40, 40, 40, 40, 1, 1, 7, 11, 11, 18, 18, 18, 18, 18, 7, 3, 1, 1, 10, 10, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 47, 48, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918076 none CC#CCC(NC(=O)C1=CC=C(OCC2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 63, 63, 40, 63, 40, 40, 40, 17, 7, 1, 1, 1, 1, 1, 1, 1, 40, 40, 113, 150, 150, 201, 201, 201, 201, 201, 113, 63, 40, 40, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 47, 48]) total number of confs: 938 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918076 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918076 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918076/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918076 Building REAL300004918077 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918077' /scratch/stefan/7775246/working/building/REAL300004918077 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918077 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918077/0 /scratch/stefan/7775246/working/building/REAL300004918077 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/78 `/scratch/stefan/7775246/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC(S(C)(=O)=O)=C1)C(=O)[O-]) `REAL300004918077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918077 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC(S(C)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 14, 5, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 31, 7, 7, 1, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 31, 45, 45, 99, 99, 99, 99, 99, 31, 7, 1, 1, 3, 3, 3, 1] 180 rigid atoms, others: [32, 36, 6, 8, 9, 10, 11, 14, 15, 16, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918077 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918077 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918077/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918077 Building REAL300004918078 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918078' /scratch/stefan/7775246/working/building/REAL300004918078 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918078 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918078/0 /scratch/stefan/7775246/working/building/REAL300004918078 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/79 `/scratch/stefan/7775246/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(C)C=C2C)O1)C(=O)[O-]) `REAL300004918078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918078 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(C)C=C2C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 32, 74, 74, 74, 74, 74, 74, 74, 1, 5, 7, 7, 12, 12, 12, 12, 12, 5, 4, 1, 1, 7, 7, 74, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918078 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(C)C=C2C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 77, 77, 74, 77, 74, 74, 74, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 128, 152, 152, 201, 201, 201, 201, 201, 128, 77, 74, 74, 27, 27, 1, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45]) total number of confs: 938 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918078 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918078 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918078/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918078 Building REAL300004918079 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918079' /scratch/stefan/7775246/working/building/REAL300004918079 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918079 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918079/0 /scratch/stefan/7775246/working/building/REAL300004918079 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/80 `/scratch/stefan/7775246/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC(C)C)C(=O)[O-]) `REAL300004918079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918079 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 37, 61, 61, 113, 113, 113, 113, 113, 37, 12, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 589 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918079 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918079 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918079/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918079 Building REAL300004918080 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918080' /scratch/stefan/7775246/working/building/REAL300004918080 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918080 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918080/0 /scratch/stefan/7775246/working/building/REAL300004918080 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/81 `/scratch/stefan/7775246/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C)N=C1C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004918080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918080 none CC#CCC(NC(=O)C1=CN(C)N=C1C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 55, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 55, 84, 84, 138, 138, 138, 138, 138, 55, 12, 1, 2, 2, 2, 7, 7, 7, 7] 199 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 683 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918080 none CC#CCC(NC(=O)C1=CN(C)N=C1C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 121, 44, 44, 7, 44, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 121, 158, 158, 200, 200, 200, 200, 200, 121, 44, 7, 7, 7, 7, 1, 1, 1, 1] 200 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 973 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918080 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918080 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918080/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918080 Building REAL300004918081 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918081' /scratch/stefan/7775246/working/building/REAL300004918081 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918081 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918081/0 /scratch/stefan/7775246/working/building/REAL300004918081 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/82 `/scratch/stefan/7775246/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2Cl)N=C1)C(=O)[O-]) `REAL300004918081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918081 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2Cl)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 20, 5, 5, 1, 5, 1, 1, 1, 1, 10, 10, 3, 8, 10, 10, 10, 1, 1, 20, 35, 35, 63, 63, 63, 63, 63, 20, 5, 1, 10, 10, 10, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918081 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2Cl)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 92, 29, 29, 10, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 92, 123, 123, 201, 201, 201, 201, 201, 92, 29, 10, 1, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 937 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918081 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918081 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918081/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918081 Building REAL300004918082 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918082' /scratch/stefan/7775246/working/building/REAL300004918082 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918082 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918082/0 /scratch/stefan/7775246/working/building/REAL300004918082 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/83 `/scratch/stefan/7775246/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2)CCCCC1)C(=O)[O-]) `REAL300004918082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918082 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 20, 5, 5, 1, 5, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 1, 1, 1, 20, 34, 34, 69, 69, 69, 69, 69, 20, 5, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 42, 43, 44, 16, 17, 18, 19, 20, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918082 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 46, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 46, 65, 65, 93, 93, 93, 93, 93, 46, 18, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 93 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 449 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918082 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918082 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918082/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918082 Building REAL300004918083 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918083' /scratch/stefan/7775246/working/building/REAL300004918083 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918083 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918083/0 /scratch/stefan/7775246/working/building/REAL300004918083 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/84 `/scratch/stefan/7775246/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(N2N=CC=C2C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918083 none CC#CCC(NC(=O)C1=CC=CC(N2N=CC=C2C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 12, 14, 14, 1, 17, 26, 26, 52, 52, 52, 52, 52, 17, 5, 1, 1, 1, 10, 10, 14, 14, 12, 14, 14, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 45, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918083 none CC#CCC(NC(=O)C1=CC=CC(N2N=CC=C2C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 111, 42, 42, 14, 42, 14, 14, 14, 14, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 14, 111, 142, 142, 201, 201, 201, 201, 201, 111, 42, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 14] 201 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 960 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918083 none CC#CCC(NC(=O)C1=CC=CC(N2N=CC=C2C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 101, 34, 34, 10, 34, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 10, 101, 138, 138, 201, 201, 201, 201, 201, 101, 34, 10, 10, 10, 1, 1, 4, 4, 3, 4, 4, 10] 201 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 979 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918083 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918083 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918083/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918083 Building REAL300004918084 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918084' /scratch/stefan/7775246/working/building/REAL300004918084 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918084 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918084/0 /scratch/stefan/7775246/working/building/REAL300004918084 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/85 `/scratch/stefan/7775246/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(OC)C=C2)C=C1)C(=O)[O-]) `REAL300004918084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918084 none CC#CCC(NC(=O)C1=NN(C2=CC=C(OC)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 35, 11, 11, 1, 11, 1, 1, 1, 1, 4, 4, 1, 1, 7, 4, 4, 1, 1, 35, 53, 53, 87, 87, 87, 87, 87, 35, 11, 4, 4, 7, 7, 7, 4, 4, 1, 1] 128 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918084 none CC#CCC(NC(=O)C1=NN(C2=CC=C(OC)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 51, 20, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 51, 73, 73, 108, 108, 108, 108, 108, 51, 20, 1, 1, 3, 3, 3, 1, 1, 4, 4] 128 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918084 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918084 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918084/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918084 Building REAL300004918085 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918085' /scratch/stefan/7775246/working/building/REAL300004918085 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918085 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918085/0 /scratch/stefan/7775246/working/building/REAL300004918085 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/86 `/scratch/stefan/7775246/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)C(C)=C1)C(=O)[O-]) `REAL300004918085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918085 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 32, 48, 48, 66, 66, 66, 66, 66, 32, 13, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 352 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918085 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Cl)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 53, 53, 7, 53, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 116, 145, 145, 201, 201, 201, 201, 201, 116, 53, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 906 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918085 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918085 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918085/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918085 Building REAL300004918086 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918086' /scratch/stefan/7775246/working/building/REAL300004918086 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918086 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918086/0 /scratch/stefan/7775246/working/building/REAL300004918086 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/87 `/scratch/stefan/7775246/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(C)C=CC(C)=C2O1)C(=O)[O-]) `REAL300004918086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918086 none CC#CCC(NC(=O)C1=C(C)C2=C(C)C=CC(C)=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 5, 1, 1, 1, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 49, 49, 67, 67, 67, 67, 67, 36, 11, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2] 67 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 348 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918086 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918086 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918086/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918086 Building REAL300004918087 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918087' /scratch/stefan/7775246/working/building/REAL300004918087 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918087 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918087/0 /scratch/stefan/7775246/working/building/REAL300004918087 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/88 `/scratch/stefan/7775246/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC2=CC(C)=C(C)C=C12)C(=O)[O-]) `REAL300004918087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918087 none CC#CCC(NC(=O)CC1=COC2=CC(C)=C(C)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 5, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 106, 50, 50, 8, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 143, 143, 201, 201, 201, 201, 201, 106, 50, 8, 8, 1, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 985 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918087 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918087 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918087/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918087 Building REAL300004918088 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918088' /scratch/stefan/7775246/working/building/REAL300004918088 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918088 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918088/0 /scratch/stefan/7775246/working/building/REAL300004918088 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/89 `/scratch/stefan/7775246/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004918088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918088 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 56, 27, 27, 5, 27, 5, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 3, 1, 56, 86, 86, 108, 108, 108, 108, 108, 56, 27, 5, 5, 1, 5, 5, 5, 3, 3, 3, 1] 201 rigid atoms, others: [33, 40, 9, 10, 11, 12, 13, 14, 15, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 565 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918088 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918088 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918088/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918088 Building REAL300004918089 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918089' /scratch/stefan/7775246/working/building/REAL300004918089 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918089 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918089/0 /scratch/stefan/7775246/working/building/REAL300004918089 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/90 `/scratch/stefan/7775246/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=CC=C1)C(C)CC)C(=O)[O-]) `REAL300004918089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918089 none CC#CCC(NC(=O)C(C1=CC=CC=C1)C(C)CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 40, 13, 13, 4, 13, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 12, 40, 66, 66, 129, 129, 129, 129, 129, 40, 13, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 12, 12] 197 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 646 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918089 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918089 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918089/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918089 Building REAL300004918090 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918090' /scratch/stefan/7775246/working/building/REAL300004918090 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918090 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918090/0 /scratch/stefan/7775246/working/building/REAL300004918090 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/91 `/scratch/stefan/7775246/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC2=C(C)C(C)=CC=C12)C(=O)[O-]) `REAL300004918090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918090 none CC#CCC(NC(=O)CC1=COC2=C(C)C(C)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 49, 49, 8, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 143, 143, 201, 201, 201, 201, 201, 108, 49, 8, 8, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 984 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918090 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918090 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918090/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918090 Building REAL300004918091 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918091' /scratch/stefan/7775246/working/building/REAL300004918091 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918091 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918091/0 /scratch/stefan/7775246/working/building/REAL300004918091 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/92 `/scratch/stefan/7775246/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC2=CC3=CC=CC=C3C=C2)O1)C(=O)[O-]) `REAL300004918091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918091 none CC#CCC(NC(=O)C1=CC=C(COC2=CC3=CC=CC=C3C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 18, 7, 8, 1, 8, 1, 1, 1, 1, 1, 8, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 18, 25, 25, 30, 30, 30, 30, 30, 18, 8, 1, 1, 8, 8, 17, 17, 17, 17, 17, 17, 17] 198 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918091 none CC#CCC(NC(=O)C1=CC=C(COC2=CC3=CC=CC=C3C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 165, 77, 78, 17, 78, 17, 17, 17, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 165, 185, 185, 198, 198, 198, 198, 198, 165, 78, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1] 198 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 848 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918091 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918091 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918091/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918091 Building REAL300004918092 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918092' /scratch/stefan/7775246/working/building/REAL300004918092 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918092 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918092/0 /scratch/stefan/7775246/working/building/REAL300004918092 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/93 `/scratch/stefan/7775246/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(CCCCCC2)S1)C(=O)[O-]) `REAL300004918092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918092 none CC#CCC(NC(=O)C1=CC2=C(CCCCCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 38, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 54, 54, 76, 76, 76, 76, 76, 38, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 389 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918092 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918092 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918092/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918092 Building REAL300004918093 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918093' /scratch/stefan/7775246/working/building/REAL300004918093 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918093 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918093/0 /scratch/stefan/7775246/working/building/REAL300004918093 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/94 `/scratch/stefan/7775246/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)C1=CC=CC=C1CC2)C(=O)[O-]) `REAL300004918093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918093 none CC#CCC(NC(=O)C1=CC2=C(S1)C1=CC=CC=C1CC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 38, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 48, 48, 67, 67, 67, 67, 67, 38, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 67 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918093 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918093 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918093/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918093 Building REAL300004918094 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918094' /scratch/stefan/7775246/working/building/REAL300004918094 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918094 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918094/0 /scratch/stefan/7775246/working/building/REAL300004918094 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/95 `/scratch/stefan/7775246/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)C1=CC=CC=C1OC2)C(=O)[O-]) `REAL300004918094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918094 none CC#CCC(NC(=O)C1=CC2=C(S1)C1=CC=CC=C1OC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 51, 51, 69, 69, 69, 69, 69, 40, 12, 1, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918094 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918094 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918094/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918094 Building REAL300004918095 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918095' /scratch/stefan/7775246/working/building/REAL300004918095 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918095 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918095/0 /scratch/stefan/7775246/working/building/REAL300004918095 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/96 `/scratch/stefan/7775246/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(CC)=C(CCC)S1)C(=O)[O-]) `REAL300004918095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918095 none CC#CCC(NC(=O)C1=CC(CC)=C(CCC)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 5, 1, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 24, 10, 10, 1, 10, 1, 1, 1, 1, 6, 1, 1, 5, 9, 1, 24, 37, 37, 61, 61, 61, 61, 61, 24, 10, 1, 6, 6, 6, 6, 6, 5, 5, 9, 9, 9, 9, 9] 201 rigid atoms, others: [6, 8, 9, 10, 11, 13, 14, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918095 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918095 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918095/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918095 Building REAL300004918096 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918096' /scratch/stefan/7775246/working/building/REAL300004918096 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918096 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918096/0 /scratch/stefan/7775246/working/building/REAL300004918096 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/97 `/scratch/stefan/7775246/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(CCC(C(C)(C)C)C2)S1)C(=O)[O-]) `REAL300004918096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918096 none CC#CCC(NC(=O)C1=CC2=C(CCC(C(C)(C)C)C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 73, 73, 36, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 36, 50, 50, 73, 73, 73, 73, 73, 36, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 78 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 46, 47, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 378 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918096 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918096 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918096/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918096 Building REAL300004918097 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918097' /scratch/stefan/7775246/working/building/REAL300004918097 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918097 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918097/0 /scratch/stefan/7775246/working/building/REAL300004918097 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/98 `/scratch/stefan/7775246/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCC)C(OC)=C1)C(=O)[O-]) `REAL300004918097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918097 none CC#CCC(NC(=O)C=CC1=CC=C(OCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 36, 18, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 9, 20, 1, 1, 3, 1, 36, 55, 55, 71, 71, 71, 71, 71, 36, 18, 5, 5, 1, 1, 20, 20, 21, 21, 21, 3, 3, 3, 1] 201 rigid atoms, others: [33, 34, 43, 9, 10, 11, 12, 13, 14, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 448 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918097 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918097 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918097/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918097 Building REAL300004918098 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918098' /scratch/stefan/7775246/working/building/REAL300004918098 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918098 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918098/0 /scratch/stefan/7775246/working/building/REAL300004918098 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/99 `/scratch/stefan/7775246/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OC)C(OCC)=C1)C(=O)[O-]) `REAL300004918098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918098 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 34, 18, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 9, 15, 1, 34, 51, 51, 78, 78, 78, 78, 78, 34, 18, 5, 5, 1, 4, 4, 4, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [34, 43, 9, 10, 11, 12, 13, 14, 15, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918098 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918098 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918098/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918098 Building REAL300004918099 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918099' /scratch/stefan/7775246/working/building/REAL300004918099 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918099 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918099/0 /scratch/stefan/7775246/working/building/REAL300004918099 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/100 `/scratch/stefan/7775246/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC1=C(C)ON=C1C)C(=O)[O-]) `REAL300004918099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918099 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=C(C)ON=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 7, 18, 60, 60, 60, 60, 60, 60, 20, 32, 32, 45, 45, 45, 45, 45, 20, 9, 1, 1, 1, 1, 18, 18, 60, 60, 60, 60, 60, 60] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918099 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=C(C)ON=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 89, 89, 60, 89, 60, 60, 60, 60, 60, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 133, 160, 160, 201, 201, 201, 201, 201, 133, 89, 60, 60, 60, 60, 9, 9, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 908 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918099 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918099 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918099/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918099 Building REAL300004918100 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918100' /scratch/stefan/7775246/working/building/REAL300004918100 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918100 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918100/0 /scratch/stefan/7775246/working/building/REAL300004918100 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/101 `/scratch/stefan/7775246/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918100 none CC#CCC(NC(=O)C(C)NC1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 10, 10, 5, 10, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 22, 22, 22, 22, 22, 17, 10, 5, 5, 5, 5, 3, 1, 1, 1, 1] 22 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918100 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918100 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918100/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918100 Building REAL300004918101 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918101' /scratch/stefan/7775246/working/building/REAL300004918101 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918101 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918101/0 /scratch/stefan/7775246/working/building/REAL300004918101 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/102 `/scratch/stefan/7775246/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=C(C)ON=C1C)C(=O)[O-]) `REAL300004918101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918101 none CC#CCC(NC(=O)CSCC1=C(C)ON=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 5, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 98, 98, 33, 98, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 144, 173, 173, 201, 201, 201, 201, 201, 144, 98, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 985 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918101 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918101 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918101/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918101 Building REAL300004918102 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918102' /scratch/stefan/7775246/working/building/REAL300004918102 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918102 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918102/0 /scratch/stefan/7775246/working/building/REAL300004918102 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/103 `/scratch/stefan/7775246/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CSC)C2=CC=CC=C2O1)C(=O)[O-]) `REAL300004918102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918102 none CC#CCC(NC(=O)C1=C(CSC)C2=CC=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 25, 10, 10, 1, 10, 1, 1, 1, 4, 23, 1, 1, 1, 1, 1, 1, 1, 25, 40, 40, 74, 74, 74, 74, 74, 25, 10, 4, 4, 24, 24, 24, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918102 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918102 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918102/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918102 Building REAL300004918103 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918103' /scratch/stefan/7775246/working/building/REAL300004918103 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918103 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918103/0 /scratch/stefan/7775246/working/building/REAL300004918103 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/104 `/scratch/stefan/7775246/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CC=CC(C)=C1)C(=O)[O-]) `REAL300004918103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918103 none CC#CCC(NC(=O)CSCC1=CC=CC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 188, 151, 151, 83, 151, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 201, 201, 201, 201, 201, 188, 151, 83, 83, 6, 6, 1, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [32, 33, 34, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918103 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918103 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918103/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918103 Building REAL300004918104 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918104' /scratch/stefan/7775246/working/building/REAL300004918104 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918104 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918104/0 /scratch/stefan/7775246/working/building/REAL300004918104 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/105 `/scratch/stefan/7775246/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CC=C(C)C=C2)CC1)C(=O)[O-]) `REAL300004918104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918104 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CC=C(C)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 31, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 12, 15, 19, 19, 1, 1, 31, 51, 51, 77, 77, 77, 77, 77, 31, 13, 1, 1, 1, 1, 1, 19, 19, 20, 20, 20, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 48, 49, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918104 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CC=C(C)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 83, 83, 19, 83, 19, 19, 19, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 136, 162, 162, 201, 201, 201, 201, 201, 136, 84, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [39, 40, 44, 12, 45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 902 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918104 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918104 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918104/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918104 Building REAL300004918105 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918105' /scratch/stefan/7775246/working/building/REAL300004918105 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918105 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918105/0 /scratch/stefan/7775246/working/building/REAL300004918105 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/106 `/scratch/stefan/7775246/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(F)C=CC=C2S1)C(=O)[O-]) `REAL300004918105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918105 none CC#CCC(NC(=O)C1=CC2=C(F)C=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 35, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 49, 49, 69, 69, 69, 69, 69, 35, 12, 1, 1, 1, 1] 69 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918105 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918105 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918105/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918105 Building REAL300004918106 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918106' /scratch/stefan/7775246/working/building/REAL300004918106 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918106 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918106/0 /scratch/stefan/7775246/working/building/REAL300004918106 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/107 `/scratch/stefan/7775246/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(Cl)C=CC=C1Cl)C(=O)[O-]) `REAL300004918106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918106 none CC#CCC(NC(=O)C=CC1=C(Cl)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 59, 24, 24, 4, 25, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 75, 75, 103, 103, 103, 103, 103, 59, 25, 4, 4, 1, 1, 1] 103 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 479 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918106 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918106 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918106/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918106 Building REAL300004918107 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918107' /scratch/stefan/7775246/working/building/REAL300004918107 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918107 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918107/0 /scratch/stefan/7775246/working/building/REAL300004918107 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/108 `/scratch/stefan/7775246/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SC(C)C)C(=O)[O-]) `REAL300004918107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918107 none CC#CCC(NC(=O)C1=CC=CC=C1SC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 31, 47, 47, 83, 83, 83, 83, 83, 31, 11, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 446 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918107 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918107 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918107/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918107 Building REAL300004918108 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918108' /scratch/stefan/7775246/working/building/REAL300004918108 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918108 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918108/0 /scratch/stefan/7775246/working/building/REAL300004918108 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/109 `/scratch/stefan/7775246/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NCC)=CC=C1C)C(=O)[O-]) `REAL300004918108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918108 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NCC)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 24, 9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 6, 20, 1, 1, 1, 1, 24, 38, 38, 59, 59, 59, 59, 59, 24, 9, 1, 6, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918108 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918108 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918108/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918108 Building REAL300004918109 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918109' /scratch/stefan/7775246/working/building/REAL300004918109 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918109 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918109/0 /scratch/stefan/7775246/working/building/REAL300004918109 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/110 `/scratch/stefan/7775246/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C)C(Cl)=C1)C(=O)[O-]) `REAL300004918109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918109 none CC#CCC(NC(=O)C=CC1=CC=C(C)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 99, 43, 43, 6, 44, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 131, 131, 173, 173, 173, 173, 173, 99, 44, 6, 6, 1, 1, 2, 2, 2, 1] 173 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 824 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918109 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918109 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918109/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918109 Building REAL300004918110 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918110' /scratch/stefan/7775246/working/building/REAL300004918110 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918110 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918110/0 /scratch/stefan/7775246/working/building/REAL300004918110 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/111 `/scratch/stefan/7775246/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004918110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918110 none CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 90, 62, 62, 13, 62, 8, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 90, 139, 139, 168, 168, 168, 168, 168, 90, 62, 13, 13, 8, 8, 1, 1, 7, 7, 1, 7, 7] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918110 none CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 119, 119, 43, 119, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 144, 181, 181, 201, 201, 201, 201, 201, 144, 119, 43, 43, 32, 32, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 980 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918110 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918110 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918110/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918110 Building REAL300004918111 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918111' /scratch/stefan/7775246/working/building/REAL300004918111 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918111 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918111/0 /scratch/stefan/7775246/working/building/REAL300004918111 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/112 `/scratch/stefan/7775246/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C12CC3CC(CC(C3)C1)C2)C(=O)[O-]) `REAL300004918111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918111 none CC#CCC(NC(=O)C1CCCN1C(=O)C12CC3CC(CC(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 33, 50, 50, 75, 75, 75, 75, 75, 33, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 118 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 381 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918111 none CC#CCC(NC(=O)C1CCCN1C(=O)C12CC3CC(CC(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 66, 25, 25, 5, 25, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 88, 88, 118, 118, 118, 118, 118, 66, 25, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 118 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 589 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918111 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918111 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918111/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918111 Building REAL300004918112 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918112' /scratch/stefan/7775246/working/building/REAL300004918112 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918112 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918112/0 /scratch/stefan/7775246/working/building/REAL300004918112 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/113 `/scratch/stefan/7775246/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=CC3=CC=CC=C32)C1)C(=O)[O-]) `REAL300004918112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918112 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=CC3=CC=CC=C32)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 28, 49, 49, 83, 83, 83, 83, 83, 28, 9, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 44, 23, 45] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 428 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918112 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=CC3=CC=CC=C32)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 49, 49, 7, 49, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 120, 155, 155, 201, 201, 201, 201, 201, 120, 49, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45]) total number of confs: 970 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918112 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918112 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918112/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918112 Building REAL300004918113 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918113' /scratch/stefan/7775246/working/building/REAL300004918113 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918113 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918113/0 /scratch/stefan/7775246/working/building/REAL300004918113 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/114 `/scratch/stefan/7775246/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CC=C1F)C(=O)[O-]) `REAL300004918113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918113 none CC#CCC(NC(=O)C1=CC(Br)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 39, 54, 54, 88, 88, 88, 88, 88, 39, 12, 1, 1, 1] 88 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918113 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918113 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918113/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918113 Building REAL300004918114 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918114' /scratch/stefan/7775246/working/building/REAL300004918114 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918114 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918114/0 /scratch/stefan/7775246/working/building/REAL300004918114 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/115 `/scratch/stefan/7775246/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918114 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 22, 10, 10, 1, 10, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 1, 1, 1, 6, 6, 2, 6, 6, 22, 35, 35, 45, 45, 45, 45, 45, 22, 10, 1, 7, 7, 11, 11, 11, 11, 11, 6, 6, 2, 6, 6] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918114 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 36, 20, 20, 6, 20, 6, 6, 6, 6, 20, 30, 30, 25, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 36, 52, 52, 59, 59, 59, 59, 59, 36, 20, 6, 20, 20, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918114 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 107, 58, 58, 11, 58, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 30, 30, 20, 30, 30, 107, 138, 138, 182, 182, 182, 182, 182, 107, 58, 11, 4, 4, 1, 1, 1, 1, 1, 30, 30, 20, 30, 30] 201 rigid atoms, others: [43, 39, 40, 41, 42, 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, 44, 45, 46, 47, 48]) total number of confs: 932 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918114 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918114 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918114/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918114 Building REAL300004918115 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918115' /scratch/stefan/7775246/working/building/REAL300004918115 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918115 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918115/0 /scratch/stefan/7775246/working/building/REAL300004918115 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/116 `/scratch/stefan/7775246/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=CC(F)=C2)=N1)C(=O)[O-]) `REAL300004918115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918115 none CC#CCC(NC(=O)CC1=CSC(C2=CC=CC(F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 51, 29, 29, 8, 29, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 51, 83, 83, 117, 117, 117, 117, 117, 51, 29, 8, 8, 1, 5, 5, 4, 5] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918115 none CC#CCC(NC(=O)CC1=CSC(C2=CC=CC(F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 70, 70, 22, 70, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 110, 157, 157, 201, 201, 201, 201, 201, 110, 70, 22, 22, 5, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1067 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918115 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918115 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918115/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918115 Building REAL300004918116 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918116' /scratch/stefan/7775246/working/building/REAL300004918116 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918116 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918116/0 /scratch/stefan/7775246/working/building/REAL300004918116 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/117 `/scratch/stefan/7775246/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-]) `REAL300004918116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918116 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 94, 44, 44, 8, 44, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 94, 137, 137, 183, 183, 183, 183, 183, 94, 44, 8, 8, 1, 4, 4, 4, 4] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 918 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918116 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 91, 91, 20, 91, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 136, 162, 162, 201, 201, 201, 201, 201, 136, 91, 20, 20, 4, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918116 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918116 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918116/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918116 Building REAL300004918117 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918117' /scratch/stefan/7775246/working/building/REAL300004918117 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918117 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918117/0 /scratch/stefan/7775246/working/building/REAL300004918117 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/118 `/scratch/stefan/7775246/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SC(F)F)C(=O)[O-]) `REAL300004918117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918117 none CC#CCC(NC(=O)C1=CC=CC=C1SC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 3, 1, 1, 1, 1, 4] 5 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918117 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918117 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918117/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918117 Building REAL300004918118 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918118' /scratch/stefan/7775246/working/building/REAL300004918118 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918118 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918118/0 /scratch/stefan/7775246/working/building/REAL300004918118 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/119 `/scratch/stefan/7775246/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)OC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918118 none CC#CCC(NC(=O)C(C)(C)OC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 111, 60, 60, 15, 60, 4, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 111, 148, 148, 201, 201, 201, 201, 201, 111, 60, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 990 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918118 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918118 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918118/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918118 Building REAL300004918119 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918119' /scratch/stefan/7775246/working/building/REAL300004918119 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918119 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918119/0 /scratch/stefan/7775246/working/building/REAL300004918119 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/120 `/scratch/stefan/7775246/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918119 none CC#CCC(NC(=O)CC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 38, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 38, 68, 68, 140, 140, 140, 140, 140, 38, 11, 4, 4, 1, 1, 3, 3, 2, 3, 3, 1, 1] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918119 none CC#CCC(NC(=O)CC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 69, 19, 19, 8, 19, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 69, 111, 111, 201, 201, 201, 201, 201, 69, 19, 8, 8, 3, 3, 1, 1, 1, 1, 1, 3, 3] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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, 40, 41]) total number of confs: 987 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918119 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918119 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918119/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918119 Building REAL300004918120 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918120' /scratch/stefan/7775246/working/building/REAL300004918120 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918120 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918120/0 /scratch/stefan/7775246/working/building/REAL300004918120 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/121 `/scratch/stefan/7775246/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(I)=C1)C(=O)[O-]) `REAL300004918120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918120 none CC#CCC(NC(=O)C1=CC=CC(I)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 18, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 27, 39, 39, 71, 71, 71, 71, 71, 27, 7, 1, 1, 1, 1] 71 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918120 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918120 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918120/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918120 Building REAL300004918121 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918121' /scratch/stefan/7775246/working/building/REAL300004918121 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918121 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918121/0 /scratch/stefan/7775246/working/building/REAL300004918121 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/122 `/scratch/stefan/7775246/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(OC)=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004918121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918121 none CC#CCC(NC(=O)CC1=CC(OC)=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 42, 15, 15, 6, 15, 1, 1, 1, 1, 1, 4, 1, 1, 6, 1, 1, 4, 1, 42, 67, 67, 108, 108, 108, 108, 108, 42, 15, 6, 6, 1, 4, 4, 4, 6, 6, 6, 4, 4, 4, 1] 201 rigid atoms, others: [33, 43, 8, 9, 10, 11, 12, 14, 15, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918121 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918121 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918121/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918121 Building REAL300004918122 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918122' /scratch/stefan/7775246/working/building/REAL300004918122 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918122 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918122/0 /scratch/stefan/7775246/working/building/REAL300004918122 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/123 `/scratch/stefan/7775246/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918122 none CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 7, 8, 19, 19, 34, 53, 53, 92, 92, 92, 92, 92, 34, 12, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918122 none CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 123, 77, 77, 19, 77, 19, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 123, 153, 153, 201, 201, 201, 201, 201, 123, 77, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [37, 38, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 939 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918122 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918122 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918122/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918122 Building REAL300004918123 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918123' /scratch/stefan/7775246/working/building/REAL300004918123 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918123 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918123/0 /scratch/stefan/7775246/working/building/REAL300004918123 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/124 `/scratch/stefan/7775246/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCCCCC)C=C1)C(=O)[O-]) `REAL300004918123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918123 none CC#CCC(NC(=O)C1=CC=C(OCCCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 11, 28, 28, 28, 1, 1, 7, 11, 11, 20, 20, 20, 20, 20, 7, 3, 1, 1, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [43, 6, 8, 9, 10, 11, 12, 44, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918123 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918123 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918123/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918123 Building REAL300004918124 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918124' /scratch/stefan/7775246/working/building/REAL300004918124 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918124 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918124/0 /scratch/stefan/7775246/working/building/REAL300004918124 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/125 `/scratch/stefan/7775246/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C([N+](=O)[O-])C=C1Cl)C(=O)[O-]) `REAL300004918124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918124 none CC#CCC(NC(=O)C1=CC=C([N+](=O)[O-])C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 31, 31, 54, 54, 54, 54, 54, 23, 7, 1, 1, 1] 54 rigid atoms, others: [6, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918124 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918124 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918124/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918124 Building REAL300004918125 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918125' /scratch/stefan/7775246/working/building/REAL300004918125 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918125 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918125/0 /scratch/stefan/7775246/working/building/REAL300004918125 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/126 `/scratch/stefan/7775246/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918125 none CC#CCC(NC(=O)CC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 66, 18, 18, 8, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 112, 112, 201, 201, 201, 201, 201, 66, 18, 8, 8, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 1006 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918125 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918125 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918125/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918125 Building REAL300004918126 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918126' /scratch/stefan/7775246/working/building/REAL300004918126 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918126 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918126/0 /scratch/stefan/7775246/working/building/REAL300004918126 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/127 `/scratch/stefan/7775246/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918126 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 11, 17, 17, 32, 32, 32, 32, 32, 11, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1] 42 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918126 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 17, 7, 7, 3, 7, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 23, 23, 42, 42, 42, 42, 42, 17, 7, 3, 3, 1, 1, 1, 1, 1, 3, 3] 42 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918126 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918126 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918126/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918126 Building REAL300004918127 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918127' /scratch/stefan/7775246/working/building/REAL300004918127 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918127 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918127/0 /scratch/stefan/7775246/working/building/REAL300004918127 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/128 `/scratch/stefan/7775246/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918127 none CC#CCC(NC(=O)C(C1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 61, 18, 18, 4, 18, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 6, 7, 7, 61, 92, 92, 150, 150, 150, 150, 150, 61, 18, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 160 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41]) total number of confs: 730 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918127 none CC#CCC(NC(=O)C(C1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 60, 18, 18, 4, 18, 1, 4, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 60, 93, 93, 154, 154, 154, 154, 154, 60, 18, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 160 rigid atoms, others: [37, 38, 39, 8, 41, 15, 16, 17, 18, 19, 20, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 753 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918127 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918127 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918127/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918127 Building REAL300004918128 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918128' /scratch/stefan/7775246/working/building/REAL300004918128 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918128 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918128/0 /scratch/stefan/7775246/working/building/REAL300004918128 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/129 `/scratch/stefan/7775246/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(OC)=C1OC)C(=O)[O-]) `REAL300004918128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918128 none CC#CCC(NC(=O)C1=CC=C(OC)C(OC)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 1, 1, 6, 1, 1, 4, 32, 56, 56, 90, 90, 90, 90, 90, 32, 12, 1, 1, 4, 4, 4, 6, 6, 6, 4, 4, 4] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 14, 15, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918128 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918128 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918128/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918128 Building REAL300004918129 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918129' /scratch/stefan/7775246/working/building/REAL300004918129 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918129 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918129/0 /scratch/stefan/7775246/working/building/REAL300004918129 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/130 `/scratch/stefan/7775246/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC=C1)C(=O)[O-]) `REAL300004918129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918129 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 9, 13, 13, 34, 51, 51, 78, 78, 78, 78, 78, 34, 12, 1, 1, 1, 1, 13, 13, 9, 13, 13] 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: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918129 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 106, 64, 64, 13, 64, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 106, 144, 144, 201, 201, 201, 201, 201, 106, 64, 13, 13, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 944 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918129 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918129 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918129/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918129 Building REAL300004918130 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918130' /scratch/stefan/7775246/working/building/REAL300004918130 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918130 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918130/0 /scratch/stefan/7775246/working/building/REAL300004918130 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/131 `/scratch/stefan/7775246/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CC=C1Cl)C(=O)[O-]) `REAL300004918130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918130 none CC#CCC(NC(=O)C1=CC(Br)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 33, 33, 64, 64, 64, 64, 64, 24, 7, 1, 1, 1] 64 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918130 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918130 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918130/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918130 Building REAL300004918131 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918131' /scratch/stefan/7775246/working/building/REAL300004918131 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918131 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918131/0 /scratch/stefan/7775246/working/building/REAL300004918131 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/132 `/scratch/stefan/7775246/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)OC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918131 none CC#CCC(NC(=O)C(C)(C)OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 58, 58, 15, 58, 4, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 110, 145, 145, 201, 201, 201, 201, 201, 110, 58, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 966 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918131 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918131 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918131/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918131 Building REAL300004918132 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918132' /scratch/stefan/7775246/working/building/REAL300004918132 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918132 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918132/0 /scratch/stefan/7775246/working/building/REAL300004918132 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/133 `/scratch/stefan/7775246/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004918132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918132 none CC#CCC(NC(=O)CC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 92, 38, 38, 6, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 137, 137, 201, 201, 201, 201, 201, 92, 38, 6, 6, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 996 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918132 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918132 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918132/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918132 Building REAL300004918133 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918133' /scratch/stefan/7775246/working/building/REAL300004918133 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918133 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918133/0 /scratch/stefan/7775246/working/building/REAL300004918133 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/134 `/scratch/stefan/7775246/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918133 none CC#CCC(NC(=O)C=CC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 114, 46, 46, 6, 47, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 114, 146, 146, 201, 201, 201, 201, 200, 114, 47, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 934 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918133 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918133 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918133/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918133 Building REAL300004918134 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918134' /scratch/stefan/7775246/working/building/REAL300004918134 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918134 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918134/0 /scratch/stefan/7775246/working/building/REAL300004918134 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/135 `/scratch/stefan/7775246/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004918134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918134 none CC#CCC(NC(=O)CC1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 47, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 47, 69, 69, 95, 95, 95, 95, 95, 47, 17, 7, 7, 1, 1, 4, 4, 4, 3, 3, 3, 1] 201 rigid atoms, others: [32, 39, 8, 9, 10, 11, 12, 13, 15, 16, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918134 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918134 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918134/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918134 Building REAL300004918135 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918135' /scratch/stefan/7775246/working/building/REAL300004918135 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918135 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918135/0 /scratch/stefan/7775246/working/building/REAL300004918135 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/136 `/scratch/stefan/7775246/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(SC)=CC=C1Cl)C(=O)[O-]) `REAL300004918135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918135 none CC#CCC(NC(=O)C1=CC(SC)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 24, 7, 7, 1, 7, 1, 1, 1, 1, 12, 1, 1, 1, 1, 24, 41, 41, 83, 83, 83, 83, 83, 24, 7, 1, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 13, 14, 15, 16, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918135 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918135 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918135/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918135 Building REAL300004918136 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918136' /scratch/stefan/7775246/working/building/REAL300004918136 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918136 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918136/0 /scratch/stefan/7775246/working/building/REAL300004918136 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/137 `/scratch/stefan/7775246/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(Cl)C=CC=C1Cl)C(=O)[O-]) `REAL300004918136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918136 none CC#CCC(NC(=O)CC1=C(Cl)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 55, 19, 18, 2, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 73, 73, 103, 103, 103, 103, 103, 55, 18, 2, 2, 1, 1, 1] 103 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918136 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918136 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918136/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918136 Building REAL300004918137 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918137' /scratch/stefan/7775246/working/building/REAL300004918137 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918137 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918137/0 /scratch/stefan/7775246/working/building/REAL300004918137 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/138 `/scratch/stefan/7775246/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918137 none CC#CCC(NC(=O)C=CC1=CC=CC=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 100, 40, 36, 6, 40, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 100, 133, 133, 191, 191, 191, 191, 191, 100, 40, 6, 6, 1, 1, 1, 1] 191 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 918 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918137 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918137 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918137/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918137 Building REAL300004918138 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918138' /scratch/stefan/7775246/working/building/REAL300004918138 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918138 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918138/0 /scratch/stefan/7775246/working/building/REAL300004918138 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/139 `/scratch/stefan/7775246/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(OC)=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004918138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918138 none CC#CCC(NC(=O)C=CC1=CC(OC)=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 37, 17, 17, 5, 17, 5, 1, 1, 1, 1, 1, 3, 1, 1, 6, 1, 1, 3, 1, 37, 56, 56, 86, 86, 86, 86, 86, 37, 17, 5, 5, 1, 3, 3, 3, 7, 7, 7, 4, 4, 4, 1] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 15, 16, 18, 19, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 432 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918138 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918138 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918138/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918138 Building REAL300004918139 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918139' /scratch/stefan/7775246/working/building/REAL300004918139 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918139 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918139/0 /scratch/stefan/7775246/working/building/REAL300004918139 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/140 `/scratch/stefan/7775246/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300004918139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918139 none CC#CCC(NC(=O)CSC1=CC2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 186, 151, 151, 40, 151, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 186, 192, 192, 201, 201, 201, 201, 201, 186, 151, 40, 40, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918139 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918139 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918139/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918139 Building REAL300004918140 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918140' /scratch/stefan/7775246/working/building/REAL300004918140 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918140 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918140/0 /scratch/stefan/7775246/working/building/REAL300004918140 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/141 `/scratch/stefan/7775246/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918140 none CC#CCC(NC(=O)C1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 31, 7, 7, 1, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 31, 43, 43, 77, 77, 77, 77, 77, 31, 7, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918140 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918140 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918140/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918140 Building REAL300004918141 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918141' /scratch/stefan/7775246/working/building/REAL300004918141 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918141 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918141/0 /scratch/stefan/7775246/working/building/REAL300004918141 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/142 `/scratch/stefan/7775246/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC=C2F)CCCC1)C(=O)[O-]) `REAL300004918141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918141 none CC#CCC(NC(=O)C1(C2=CC=CC=C2F)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 37, 11, 11, 1, 11, 1, 1, 9, 9, 3, 9, 9, 9, 1, 1, 1, 1, 37, 62, 62, 109, 109, 109, 109, 109, 37, 11, 9, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1] 180 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 16, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 551 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918141 none CC#CCC(NC(=O)C1(C2=CC=CC=C2F)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 77, 29, 29, 9, 29, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 77, 113, 113, 180, 180, 180, 180, 180, 77, 29, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 180 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 862 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918141 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918141 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918141/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918141 Building REAL300004918142 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918142' /scratch/stefan/7775246/working/building/REAL300004918142 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918142 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918142/0 /scratch/stefan/7775246/working/building/REAL300004918142 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/143 `/scratch/stefan/7775246/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(F)=C2)CCCC1)C(=O)[O-]) `REAL300004918142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918142 none CC#CCC(NC(=O)C1(C2=CC=CC(F)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 32, 11, 11, 1, 11, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 32, 53, 53, 95, 95, 95, 95, 95, 32, 11, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 16, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 470 number of broken/clashed sets: 189 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918142 none CC#CCC(NC(=O)C1(C2=CC=CC(F)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 86, 35, 35, 9, 35, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 86, 130, 130, 201, 201, 201, 201, 201, 86, 35, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1006 number of broken/clashed sets: 189 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918142 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918142 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918142/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918142 Building REAL300004918143 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918143' /scratch/stefan/7775246/working/building/REAL300004918143 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918143 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918143/0 /scratch/stefan/7775246/working/building/REAL300004918143 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/144 `/scratch/stefan/7775246/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918143 none CC#CCC(NC(=O)C1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 12, 30, 30, 30, 1, 1, 13, 23, 23, 54, 54, 54, 54, 54, 13, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918143 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918143 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918143/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918143 Building REAL300004918144 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918144' /scratch/stefan/7775246/working/building/REAL300004918144 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918144 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918144/0 /scratch/stefan/7775246/working/building/REAL300004918144 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/145 `/scratch/stefan/7775246/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCCC2)=C1)C(=O)[O-]) `REAL300004918144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918144 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 22, 22, 22, 1, 16, 24, 24, 45, 45, 45, 45, 45, 16, 5, 1, 1, 1, 22, 22, 22, 23, 22, 23, 23, 22, 22, 22, 22, 22, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 49, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918144 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 65, 65, 23, 65, 23, 23, 23, 22, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 22, 130, 159, 159, 201, 201, 201, 201, 201, 130, 65, 23, 23, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 201 rigid atoms, others: [48, 37, 38, 39, 40, 41, 42, 43, 44, 13, 46, 45, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49]) total number of confs: 950 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918144 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918144 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918144/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918144 Building REAL300004918145 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918145' /scratch/stefan/7775246/working/building/REAL300004918145 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918145 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918145/0 /scratch/stefan/7775246/working/building/REAL300004918145 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/146 `/scratch/stefan/7775246/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)N(C1=CC=CC=C1)N=C2C)C(=O)[O-]) `REAL300004918145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918145 none CC#CCC(NC(=O)C1=CC2=C(S1)N(C1=CC=CC=C1)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 47, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 47, 71, 71, 124, 124, 124, 124, 124, 47, 13, 1, 6, 6, 1, 6, 6, 2, 2, 2] 133 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 601 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918145 none CC#CCC(NC(=O)C1=CC2=C(S1)N(C1=CC=CC=C1)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 90, 40, 40, 6, 40, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 90, 109, 109, 133, 133, 133, 133, 133, 90, 40, 6, 1, 1, 1, 1, 1, 6, 6, 6] 133 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918145 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918145 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918145/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918145 Building REAL300004918146 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918146' /scratch/stefan/7775246/working/building/REAL300004918146 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918146 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918146/0 /scratch/stefan/7775246/working/building/REAL300004918146 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/147 `/scratch/stefan/7775246/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)ON=C1C1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918146 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 44, 68, 68, 98, 98, 98, 98, 98, 44, 12, 2, 2, 2, 9, 9, 2, 9] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918146 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 55, 55, 9, 55, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 118, 154, 154, 201, 201, 201, 201, 201, 118, 55, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 950 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918146 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918146 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918146/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918146 Building REAL300004918147 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918147' /scratch/stefan/7775246/working/building/REAL300004918147 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918147 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918147/0 /scratch/stefan/7775246/working/building/REAL300004918147 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/148 `/scratch/stefan/7775246/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCOCC2)C=C1)C(=O)[O-]) `REAL300004918147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918147 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 33, 33, 33, 33, 33, 1, 1, 9, 15, 15, 32, 32, 32, 32, 32, 9, 3, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 43, 6, 8, 9, 10, 11, 12, 44, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918147 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 132, 62, 62, 33, 62, 33, 33, 33, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 33, 33, 132, 157, 157, 201, 201, 201, 201, 201, 132, 62, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 944 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918147 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918147 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918147/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918147 Building REAL300004918148 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918148' /scratch/stefan/7775246/working/building/REAL300004918148 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918148 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918148/0 /scratch/stefan/7775246/working/building/REAL300004918148 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/149 `/scratch/stefan/7775246/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCCC2)C=C1)C(=O)[O-]) `REAL300004918148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918148 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 33, 33, 33, 33, 33, 1, 1, 9, 15, 15, 31, 31, 31, 31, 31, 9, 3, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 45, 46, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918148 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 58, 58, 6, 58, 6, 32, 32, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 32, 32, 126, 157, 157, 201, 201, 201, 201, 201, 126, 58, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 15, 16, 17, 18, 19, 20, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46]) total number of confs: 1010 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918148 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918148 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918148/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918148 Building REAL300004918149 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918149' /scratch/stefan/7775246/working/building/REAL300004918149 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918149 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918149/0 /scratch/stefan/7775246/working/building/REAL300004918149 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/150 `/scratch/stefan/7775246/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(CC)CC)C=C1)C(=O)[O-]) `REAL300004918149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918149 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(CC)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 18, 39, 18, 41, 1, 1, 7, 11, 11, 21, 21, 21, 21, 21, 7, 3, 1, 1, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918149 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918149 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918149/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918149 Building REAL300004918150 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918150' /scratch/stefan/7775246/working/building/REAL300004918150 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918150 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918150/0 /scratch/stefan/7775246/working/building/REAL300004918150 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/151 `/scratch/stefan/7775246/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918150 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 52, 12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 7, 7, 1, 7, 7, 52, 80, 80, 151, 151, 151, 151, 151, 52, 12, 1, 4, 4, 1, 4, 4, 7, 7, 1, 7, 7] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 725 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918150 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 110, 42, 42, 7, 42, 7, 7, 7, 7, 17, 17, 7, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 110, 143, 143, 200, 200, 200, 200, 200, 110, 42, 7, 17, 17, 7, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 959 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918150 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 81, 32, 32, 3, 31, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 17, 17, 4, 17, 17, 81, 110, 110, 176, 176, 176, 176, 176, 81, 32, 4, 1, 1, 1, 1, 1, 17, 17, 4, 17, 17] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 842 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918150 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918150 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918150/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918150 Building REAL300004918151 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918151' /scratch/stefan/7775246/working/building/REAL300004918151 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918151 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918151/0 /scratch/stefan/7775246/working/building/REAL300004918151 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/152 `/scratch/stefan/7775246/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)C(C)=C1)C(=O)[O-]) `REAL300004918151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918151 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 49, 76, 76, 128, 128, 128, 128, 128, 49, 12, 2, 2, 2, 4, 4, 1, 4, 4, 2, 2, 2, 1] 152 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 628 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918151 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 80, 27, 27, 4, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 80, 110, 110, 152, 152, 152, 152, 152, 80, 27, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4] 152 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 729 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918151 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918151 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918151/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918151 Building REAL300004918152 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918152' /scratch/stefan/7775246/working/building/REAL300004918152 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918152 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918152/0 /scratch/stefan/7775246/working/building/REAL300004918152 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/153 `/scratch/stefan/7775246/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004918152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918152 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 42, 11, 11, 1, 11, 1, 1, 1, 1, 1, 4, 4, 2, 3, 4, 4, 1, 1, 1, 42, 69, 69, 107, 107, 107, 107, 107, 42, 11, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 1] 141 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 554 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918152 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 72, 24, 24, 4, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 72, 92, 92, 141, 141, 141, 141, 141, 72, 24, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 141 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 648 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918152 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918152 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918152/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918152 Building REAL300004918153 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918153' /scratch/stefan/7775246/working/building/REAL300004918153 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918153 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918153/0 /scratch/stefan/7775246/working/building/REAL300004918153 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/154 `/scratch/stefan/7775246/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918153 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 46, 21, 21, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 20, 20, 20, 20, 20, 46, 48, 48, 63, 63, 63, 63, 63, 46, 21, 7, 2, 2, 1, 1, 1, 1, 1, 13, 20, 20, 20, 20, 20] 71 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918153 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 51, 29, 29, 7, 29, 3, 7, 19, 20, 20, 19, 20, 20, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 52, 52, 62, 62, 62, 62, 62, 51, 29, 7, 19, 19, 20, 20, 20, 20, 20, 3, 1, 1, 1, 1, 1] 71 rigid atoms, others: [44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918153 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918153 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918153/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918153 Building REAL300004918154 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918154' /scratch/stefan/7775246/working/building/REAL300004918154 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918154 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918154/0 /scratch/stefan/7775246/working/building/REAL300004918154 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/155 `/scratch/stefan/7775246/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(SC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918154 none CC#CCC(NC(=O)C(SC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 105, 59, 59, 17, 59, 7, 1, 1, 1, 1, 1, 1, 1, 17, 32, 32, 22, 32, 32, 105, 141, 141, 189, 189, 189, 189, 189, 105, 59, 17, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32] 201 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 958 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918154 none CC#CCC(NC(=O)C(SC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 38, 19, 19, 4, 19, 1, 4, 15, 32, 32, 15, 32, 32, 1, 1, 1, 1, 1, 1, 38, 56, 56, 105, 105, 105, 105, 105, 38, 19, 4, 32, 32, 19, 32, 32, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 8, 41, 42, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 570 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918154 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918154 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918154/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918154 Building REAL300004918155 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918155' /scratch/stefan/7775246/working/building/REAL300004918155 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918155 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918155/0 /scratch/stefan/7775246/working/building/REAL300004918155 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/156 `/scratch/stefan/7775246/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300004918155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918155 none CC#CCC(NC(=O)COC1=CC2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 110, 71, 71, 19, 71, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 116, 116, 127, 127, 127, 127, 127, 110, 71, 19, 19, 1, 1, 1, 1, 1, 1, 1] 127 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 531 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918155 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918155 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918155/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918155 Building REAL300004918156 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918156' /scratch/stefan/7775246/working/building/REAL300004918156 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918156 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918156/0 /scratch/stefan/7775246/working/building/REAL300004918156 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/157 `/scratch/stefan/7775246/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004918156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918156 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 21, 36, 36, 59, 59, 59, 59, 59, 21, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19] 171 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918156 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 103, 61, 61, 19, 61, 19, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 103, 140, 140, 171, 171, 171, 171, 171, 103, 61, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1] 171 rigid atoms, others: [37, 38, 39, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 853 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918156 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918156 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918156/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918156 Building REAL300004918157 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918157' /scratch/stefan/7775246/working/building/REAL300004918157 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918157 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918157/0 /scratch/stefan/7775246/working/building/REAL300004918157 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/158 `/scratch/stefan/7775246/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CC3CC(C1)CC(C1=CC=C(C)C=C1)(C3)C2)C(=O)[O-]) `REAL300004918157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918157 none CC#CCC(NC(=O)C12CC3CC(C1)CC(C1=CC=C(C)C=C1)(C3)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 31, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 1, 1, 31, 55, 55, 146, 146, 146, 146, 146, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 200 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918157 none CC#CCC(NC(=O)C12CC3CC(C1)CC(C1=CC=C(C)C=C1)(C3)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 81, 20, 20, 5, 20, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 81, 121, 121, 200, 200, 200, 200, 200, 81, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5] 200 rigid atoms, others: [51, 50, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 52, 53, 54, 55]) total number of confs: 979 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918157 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918157 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918157/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918157 Building REAL300004918158 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918158' /scratch/stefan/7775246/working/building/REAL300004918158 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918158 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918158/0 /scratch/stefan/7775246/working/building/REAL300004918158 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/159 `/scratch/stefan/7775246/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004918158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918158 none CC#CCC(NC(=O)COC1=CC=CC=C1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 109, 83, 83, 26, 83, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 8, 10, 10, 109, 109, 109, 128, 128, 128, 128, 128, 109, 83, 26, 26, 1, 1, 1, 1, 7, 7, 10, 10, 7, 10, 10] 201 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918158 none CC#CCC(NC(=O)COC1=CC=CC=C1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 176, 176, 86, 176, 36, 10, 10, 10, 6, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 86, 86, 10, 9, 10, 10, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 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: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918158 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918158 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918158/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918158 Building REAL300004918159 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918159' /scratch/stefan/7775246/working/building/REAL300004918159 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918159 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918159/0 /scratch/stefan/7775246/working/building/REAL300004918159 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/160 `/scratch/stefan/7775246/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(F)C=C2)O1)C(=O)[O-]) `REAL300004918159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918159 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(F)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 1, 24, 39, 39, 75, 75, 75, 75, 75, 24, 10, 1, 1, 8, 8, 15, 15, 15, 14] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 381 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918159 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(F)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 56, 56, 14, 56, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 113, 148, 148, 201, 201, 201, 201, 201, 113, 56, 14, 15, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 975 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918159 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918159 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918159/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918159 Building REAL300004918160 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918160' /scratch/stefan/7775246/working/building/REAL300004918160 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918160 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918160/0 /scratch/stefan/7775246/working/building/REAL300004918160 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/161 `/scratch/stefan/7775246/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN2C(=N1)N=C(C)C=C2C)C(=O)[O-]) `REAL300004918160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918160 none CC#CCC(NC(=O)C1=NN2C(=N1)N=C(C)C=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 8, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 70, 70, 70, 70, 70, 37, 12, 2, 2, 2, 1, 2, 2, 2] 70 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918160 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918160 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918160/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918160 Building REAL300004918161 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918161' /scratch/stefan/7775246/working/building/REAL300004918161 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918161 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918161/0 /scratch/stefan/7775246/working/building/REAL300004918161 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/162 `/scratch/stefan/7775246/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)NC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300004918161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918161 none CC#CCC(NC(=O)C1CCCN(C(=O)NC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 20, 21, 21, 21, 21, 21, 1, 24, 39, 39, 65, 65, 65, 65, 65, 24, 11, 1, 1, 1, 1, 1, 1, 1, 20, 21, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 46, 47, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45]) total number of confs: 364 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918161 none CC#CCC(NC(=O)C1CCCN(C(=O)NC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 76, 76, 21, 76, 21, 21, 21, 21, 8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 21, 133, 158, 158, 201, 201, 201, 201, 201, 133, 76, 21, 21, 21, 21, 21, 21, 21, 4, 1, 1, 1, 1, 1, 21, 21] 201 rigid atoms, others: [41, 42, 43, 44, 45, 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, 46, 47]) total number of confs: 907 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918161 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918161 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918161/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918161 Building REAL300004918162 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918162' /scratch/stefan/7775246/working/building/REAL300004918162 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918162 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918162/0 /scratch/stefan/7775246/working/building/REAL300004918162 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/163 `/scratch/stefan/7775246/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(S(N)(=O)=O)=C1)C(=O)[O-]) `REAL300004918162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918162 none CC#CCC(NC(=O)C1=CC=C(C)C(S(N)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 14, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 26, 39, 39, 77, 77, 77, 77, 77, 26, 7, 1, 1, 2, 2, 2, 2, 2, 1] 77 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 14, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918162 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918162 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918162/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918162 Building REAL300004918163 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918163' /scratch/stefan/7775246/working/building/REAL300004918163 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918163 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918163/0 /scratch/stefan/7775246/working/building/REAL300004918163 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/164 `/scratch/stefan/7775246/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(C2=CC=C(F)C=C2)NC2=CC=CC=C21)C(=O)[O-]) `REAL300004918163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918163 none CC#CCC(NC(=O)CCC1=C(C2=CC=C(F)C=C2)NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 94, 22, 22, 5, 22, 3, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 96, 137, 137, 197, 197, 197, 195, 197, 96, 23, 5, 5, 3, 3, 4, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 45, 46, 44, 48, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 982 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918163 none CC#CCC(NC(=O)CCC1=C(C2=CC=C(F)C=C2)NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 50, 50, 12, 50, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 148, 170, 170, 201, 201, 201, 199, 201, 148, 50, 12, 12, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 961 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918163 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918163 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918163/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918163 Building REAL300004918164 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918164' /scratch/stefan/7775246/working/building/REAL300004918164 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918164 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918164/0 /scratch/stefan/7775246/working/building/REAL300004918164 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/165 `/scratch/stefan/7775246/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004918164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918164 none CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 118, 57, 57, 6, 57, 6, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 118, 148, 148, 199, 199, 199, 199, 199, 118, 57, 6, 6, 1, 4, 4, 1, 4, 4, 1] 201 rigid atoms, others: [33, 39, 9, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 913 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918164 none CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 138, 83, 83, 19, 83, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 138, 165, 165, 201, 201, 201, 201, 201, 138, 83, 19, 19, 4, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 890 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918164 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918164 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918164/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918164 Building REAL300004918165 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918165' /scratch/stefan/7775246/working/building/REAL300004918165 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918165 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918165/0 /scratch/stefan/7775246/working/building/REAL300004918165 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/166 `/scratch/stefan/7775246/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=C(C)C=C2)O1)C(=O)[O-]) `REAL300004918165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918165 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=C(C)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 41, 41, 15, 15, 41, 41, 13, 20, 20, 20, 40, 40, 40, 40, 40, 20, 11, 1, 1, 1, 1, 13, 41, 41, 41, 41, 41, 41, 41] 95 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918165 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=C(C)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 88, 76, 76, 41, 76, 41, 41, 41, 41, 41, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 88, 88, 88, 95, 95, 95, 95, 95, 88, 76, 41, 41, 41, 41, 6, 1, 1, 2, 2, 2, 1, 1] 95 rigid atoms, others: [41, 42, 46, 47, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918165 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=C(C)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 67, 52, 52, 13, 52, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 2, 2, 6, 6, 1, 67, 67, 67, 89, 89, 89, 89, 89, 67, 52, 13, 13, 13, 13, 1, 6, 6, 6, 6, 6, 6, 6] 95 rigid atoms, others: [40, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918165 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918165 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918165/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918165 Building REAL300004918166 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918166' /scratch/stefan/7775246/working/building/REAL300004918166 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918166 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918166/0 /scratch/stefan/7775246/working/building/REAL300004918166 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/167 `/scratch/stefan/7775246/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(CC)OC2=CC=CC=C21)C(=O)[O-]) `REAL300004918166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918166 none CC#CCC(NC(=O)C=CC1=C(CC)OC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 67, 35, 35, 9, 35, 9, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 67, 96, 96, 122, 122, 122, 122, 122, 67, 35, 9, 9, 5, 5, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918166 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918166 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918166/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918166 Building REAL300004918167 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918167' /scratch/stefan/7775246/working/building/REAL300004918167 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918167 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918167/0 /scratch/stefan/7775246/working/building/REAL300004918167 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/168 `/scratch/stefan/7775246/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(Br)C(OC)=C1)C(=O)[O-]) `REAL300004918167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918167 none CC#CCC(NC(=O)C1=CC(OC)=C(Br)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 17, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 26, 7, 7, 1, 7, 1, 1, 1, 1, 3, 1, 1, 1, 1, 3, 1, 26, 45, 45, 97, 97, 97, 97, 97, 26, 7, 1, 4, 4, 4, 4, 4, 4, 1] 168 rigid atoms, others: [36, 6, 8, 9, 10, 11, 13, 14, 15, 16, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918167 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918167 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918167/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918167 Building REAL300004918168 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918168' /scratch/stefan/7775246/working/building/REAL300004918168 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918168 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918168/0 /scratch/stefan/7775246/working/building/REAL300004918168 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/169 `/scratch/stefan/7775246/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918168 none CC#CCC(NC(=O)C1=CC=C(SC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 12, 26, 26, 26, 1, 1, 14, 23, 23, 57, 57, 57, 57, 57, 14, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918168 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918168 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918168/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918168 Building REAL300004918169 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918169' /scratch/stefan/7775246/working/building/REAL300004918169 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918169 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918169/0 /scratch/stefan/7775246/working/building/REAL300004918169 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/170 `/scratch/stefan/7775246/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC(OC)=CC(OC)=C1)C(=O)[O-]) `REAL300004918169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918169 none CC#CCC(NC(=O)CCC1=CC(OC)=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 33, 15, 15, 6, 15, 3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 2, 1, 33, 40, 40, 63, 63, 63, 63, 63, 33, 15, 6, 6, 3, 3, 1, 3, 3, 3, 1, 2, 3, 2, 1] 99 rigid atoms, others: [34, 38, 9, 10, 11, 12, 13, 15, 16, 17, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918169 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918169 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918169/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918169 Building REAL300004918170 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918170' /scratch/stefan/7775246/working/building/REAL300004918170 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918170 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918170/0 /scratch/stefan/7775246/working/building/REAL300004918170 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/171 `/scratch/stefan/7775246/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2N=NC3=CC=CC=C32)C=C1)C(=O)[O-]) `REAL300004918170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918170 none CC#CCC(NC(=O)C1=CC=C(CN2N=NC3=CC=CC=C32)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 9, 14, 14, 26, 26, 26, 26, 26, 9, 3, 1, 1, 6, 6, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918170 none CC#CCC(NC(=O)C1=CC=C(CN2N=NC3=CC=CC=C32)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 45, 45, 25, 45, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 111, 144, 144, 201, 201, 201, 201, 201, 111, 45, 25, 25, 7, 7, 1, 1, 1, 1, 25, 25] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 971 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918170 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918170 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918170/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918170 Building REAL300004918171 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918171' /scratch/stefan/7775246/working/building/REAL300004918171 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918171 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918171/0 /scratch/stefan/7775246/working/building/REAL300004918171 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/172 `/scratch/stefan/7775246/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(C)N(CC(C)C)N=C1C)C(=O)[O-]) `REAL300004918171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918171 none CC#CCC(NC(=O)CCC1=C(C)N(CC(C)C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 45, 20, 20, 3, 19, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 45, 74, 74, 105, 105, 105, 105, 105, 45, 20, 4, 4, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918171 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918171 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918171/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918171 Building REAL300004918172 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918172' /scratch/stefan/7775246/working/building/REAL300004918172 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918172 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918172/0 /scratch/stefan/7775246/working/building/REAL300004918172 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/173 `/scratch/stefan/7775246/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004918172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918172 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 55, 13, 13, 1, 13, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 3, 3, 2, 3, 3, 1, 55, 82, 82, 154, 154, 154, 154, 154, 55, 13, 6, 6, 1, 6, 6, 3, 3, 3, 3, 3] 177 rigid atoms, others: [6, 8, 9, 10, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918172 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 105, 34, 34, 3, 34, 3, 3, 3, 13, 13, 4, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 3, 105, 130, 130, 174, 174, 174, 174, 174, 105, 34, 13, 13, 5, 13, 13, 1, 1, 1, 1, 1] 177 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 835 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918172 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 90, 33, 33, 6, 33, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 12, 13, 13, 6, 90, 116, 116, 169, 169, 169, 169, 169, 90, 33, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 177 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918172 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918172 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918172/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918172 Building REAL300004918173 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918173' /scratch/stefan/7775246/working/building/REAL300004918173 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918173 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918173/0 /scratch/stefan/7775246/working/building/REAL300004918173 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/174 `/scratch/stefan/7775246/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COC2=CC=C(Cl)C=C2C1)C(=O)[O-]) `REAL300004918173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918173 none CC#CCC(NC(=O)C1COC2=CC=C(Cl)C=C2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 45, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 64, 64, 89, 89, 89, 89, 89, 45, 13, 1, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 445 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918173 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918173 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918173/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918173 Building REAL300004918174 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918174' /scratch/stefan/7775246/working/building/REAL300004918174 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918174 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918174/0 /scratch/stefan/7775246/working/building/REAL300004918174 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/175 `/scratch/stefan/7775246/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC(=O)C1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004918174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918174 none CC#CCC(NC(=O)CCCNC(=O)C1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 158, 117, 117, 54, 118, 38, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 15, 158, 165, 165, 175, 175, 175, 175, 175, 158, 118, 53, 54, 40, 40, 29, 29, 11, 1, 1, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918174 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918174 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918174/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918174 Building REAL300004918175 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918175' /scratch/stefan/7775246/working/building/REAL300004918175 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918175 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918175/0 /scratch/stefan/7775246/working/building/REAL300004918175 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/176 `/scratch/stefan/7775246/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CSC(C)=N2)=CN1)C(=O)[O-]) `REAL300004918175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918175 none CC#CCC(NC(=O)C1=CC(C2=CSC(C)=N2)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 1, 5, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 30, 13, 13, 1, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 30, 48, 48, 84, 84, 84, 84, 84, 30, 13, 1, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918175 none CC#CCC(NC(=O)C1=CC(C2=CSC(C)=N2)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 1, 5, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 69, 69, 13, 69, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 124, 154, 154, 201, 201, 201, 201, 201, 124, 69, 13, 1, 2, 2, 2, 13, 13] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 915 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918175 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918175 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918175/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918175 Building REAL300004918176 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918176' /scratch/stefan/7775246/working/building/REAL300004918176 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918176 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918176/0 /scratch/stefan/7775246/working/building/REAL300004918176 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/177 `/scratch/stefan/7775246/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(OC)C(OC)=C2)=N1)C(=O)[O-]) `REAL300004918176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918176 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(OC)C(OC)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 4, 4, 13, 5, 5, 13, 5, 1, 16, 25, 25, 47, 47, 47, 47, 47, 16, 7, 1, 5, 5, 13, 13, 13, 13, 13, 13, 5] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918176 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(OC)C(OC)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 45, 19, 19, 5, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 5, 45, 73, 73, 125, 125, 125, 125, 125, 45, 19, 5, 1, 1, 4, 4, 4, 3, 3, 3, 1] 201 rigid atoms, others: [34, 35, 42, 11, 12, 13, 14, 15, 16, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918176 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918176 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918176/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918176 Building REAL300004918177 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918177' /scratch/stefan/7775246/working/building/REAL300004918177 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918177 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918177/0 /scratch/stefan/7775246/working/building/REAL300004918177 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/178 `/scratch/stefan/7775246/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-]) `REAL300004918177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918177 none CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 77, 57, 57, 15, 57, 8, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 77, 100, 100, 104, 104, 104, 104, 104, 77, 57, 15, 15, 8, 8, 1, 1, 12, 12, 10, 12] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918177 none CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 136, 136, 55, 136, 40, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 169, 188, 188, 201, 201, 201, 201, 201, 169, 136, 55, 55, 40, 40, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918177 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918177 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918177/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918177 Building REAL300004918178 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918178' /scratch/stefan/7775246/working/building/REAL300004918178 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918178 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918178/0 /scratch/stefan/7775246/working/building/REAL300004918178 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/179 `/scratch/stefan/7775246/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCCCC)C(OC)=C1)C(=O)[O-]) `REAL300004918178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918178 none CC#CCC(NC(=O)C=CC1=CC=C(OCCCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 22, 18, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 10, 28, 50, 50, 1, 1, 3, 1, 22, 22, 22, 26, 26, 26, 26, 26, 22, 18, 5, 5, 1, 1, 28, 28, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 49, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 286 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918178 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918178 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918178/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918178 Building REAL300004918179 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918179' /scratch/stefan/7775246/working/building/REAL300004918179 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918179 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918179/0 /scratch/stefan/7775246/working/building/REAL300004918179 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/180 `/scratch/stefan/7775246/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(OCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004918179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918179 none CC#CCC(NC(=O)C1=CC(Cl)=C(OCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 8, 16, 1, 1, 9, 12, 1, 11, 17, 17, 31, 31, 31, 31, 31, 11, 5, 1, 8, 8, 17, 17, 18, 18, 18, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 45, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918179 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918179 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918179/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918179 Building REAL300004918180 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918180' /scratch/stefan/7775246/working/building/REAL300004918180 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918180 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918180/0 /scratch/stefan/7775246/working/building/REAL300004918180 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/181 `/scratch/stefan/7775246/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918180 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 33, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 33, 48, 48, 71, 71, 71, 71, 71, 33, 11, 2, 2, 2, 3, 3, 1, 3, 3] 72 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 367 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918180 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 46, 25, 25, 3, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 46, 57, 57, 72, 72, 72, 72, 72, 46, 25, 4, 4, 4, 1, 1, 1, 1, 1] 72 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 329 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918180 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918180 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918180/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918180 Building REAL300004918181 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918181' /scratch/stefan/7775246/working/building/REAL300004918181 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918181 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918181/0 /scratch/stefan/7775246/working/building/REAL300004918181 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/182 `/scratch/stefan/7775246/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C(C)=O)C=C2)O1)C(=O)[O-]) `REAL300004918181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918181 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C(C)=O)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 21, 9, 8, 1, 8, 1, 1, 1, 1, 1, 7, 7, 1, 1, 12, 12, 7, 7, 1, 21, 35, 35, 53, 53, 53, 53, 53, 21, 9, 1, 1, 7, 7, 14, 13, 13, 7, 7] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918181 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C(C)=O)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 73, 34, 34, 7, 34, 7, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 7, 73, 101, 101, 137, 137, 137, 137, 137, 73, 34, 7, 7, 1, 1, 13, 13, 13, 1, 1] 201 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918181 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918181 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918181/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918181 Building REAL300004918182 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918182' /scratch/stefan/7775246/working/building/REAL300004918182 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918182 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918182/0 /scratch/stefan/7775246/working/building/REAL300004918182 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/183 `/scratch/stefan/7775246/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1N1CCC(C)CC1)C(=O)[O-]) `REAL300004918182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918182 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1N1CCC(C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 30, 39, 39, 50, 50, 50, 50, 50, 30, 12, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918182 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1N1CCC(C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 16, 16, 3, 16, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 33, 41, 41, 50, 50, 50, 50, 50, 33, 16, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [48, 37, 38, 39, 40, 41, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918182 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918182 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918182/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918182 Building REAL300004918183 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918183' /scratch/stefan/7775246/working/building/REAL300004918183 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918183 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918183/0 /scratch/stefan/7775246/working/building/REAL300004918183 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/184 `/scratch/stefan/7775246/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=NC3=CC=CC=C3S2)O1)C(=O)[O-]) `REAL300004918183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918183 none CC#CCC(NC(=O)C1=CC=C(C2=NC3=CC=CC=C3S2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 36, 56, 56, 93, 93, 93, 93, 93, 36, 12, 1, 1, 13, 13, 12, 13] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918183 none CC#CCC(NC(=O)C1=CC=C(C2=NC3=CC=CC=C3S2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 67, 67, 13, 67, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 127, 161, 161, 201, 201, 201, 201, 201, 127, 67, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 920 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918183 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918183 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918183/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918183 Building REAL300004918184 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918184' /scratch/stefan/7775246/working/building/REAL300004918184 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918184 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918184/0 /scratch/stefan/7775246/working/building/REAL300004918184 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/185 `/scratch/stefan/7775246/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2SCCS2)C=C1)C(=O)[O-]) `REAL300004918184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918184 none CC#CCC(NC(=O)C1=CC=C(C2SCCS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 5, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 12, 21, 21, 39, 39, 39, 39, 39, 12, 4, 1, 1, 13, 13, 13, 13, 13, 1, 1] 110 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918184 none CC#CCC(NC(=O)C1=CC=C(C2SCCS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 5, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 54, 20, 20, 3, 20, 3, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 54, 68, 68, 110, 110, 110, 110, 110, 54, 20, 13, 13, 1, 1, 1, 1, 1, 13, 13] 110 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918184 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918184 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918184/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918184 Building REAL300004918185 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918185' /scratch/stefan/7775246/working/building/REAL300004918185 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918185 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918185/0 /scratch/stefan/7775246/working/building/REAL300004918185 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/186 `/scratch/stefan/7775246/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(C)(=O)=O)C=C1)C(=O)[O-]) `REAL300004918185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918185 none CC#CCC(NC(=O)C1=CC=C(S(C)(=O)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 16, 22, 22, 39, 39, 39, 39, 39, 16, 4, 1, 1, 3, 3, 3, 1, 1] 66 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918185 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918185 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918185/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918185 Building REAL300004918186 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918186' /scratch/stefan/7775246/working/building/REAL300004918186 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918186 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918186/0 /scratch/stefan/7775246/working/building/REAL300004918186 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/187 `/scratch/stefan/7775246/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CS(C)(=O)=O)C=C1)C(=O)[O-]) `REAL300004918186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918186 none CC#CCC(NC(=O)C1=CC=C(CS(C)(=O)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 27, 27, 27, 1, 1, 9, 14, 14, 32, 32, 32, 32, 32, 9, 3, 1, 1, 7, 7, 27, 27, 27, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918186 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918186 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918186/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918186 Building REAL300004918187 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918187' /scratch/stefan/7775246/working/building/REAL300004918187 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918187 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918187/0 /scratch/stefan/7775246/working/building/REAL300004918187 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/188 `/scratch/stefan/7775246/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCC)C(OCC)=C1)C(=O)[O-]) `REAL300004918187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918187 none CC#CCC(NC(=O)C=CC1=CC=C(OCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 38, 21, 21, 5, 21, 5, 1, 1, 1, 1, 1, 1, 9, 12, 1, 1, 9, 12, 1, 38, 54, 54, 75, 75, 75, 75, 75, 38, 21, 5, 5, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 17, 18, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 430 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918187 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918187 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918187/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918187 Building REAL300004918188 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918188' /scratch/stefan/7775246/working/building/REAL300004918188 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918188 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918188/0 /scratch/stefan/7775246/working/building/REAL300004918188 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/189 `/scratch/stefan/7775246/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(=CC1=CC=CO1)N1N=NN=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918188 none CC#CCC(NC(=O)C(=CC1=CC=CO1)N1N=NN=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 14, 12, 12, 7, 12, 7, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 20, 14, 12, 7, 1, 1, 1, 14, 14, 14, 14, 14] 20 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918188 none CC#CCC(NC(=O)C(=CC1=CC=CO1)N1N=NN=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 11, 11, 7, 11, 4, 7, 7, 14, 14, 14, 14, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 17, 17, 17, 17, 17, 15, 11, 7, 14, 14, 14, 1, 1, 1, 1, 1] 20 rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918188 none CC#CCC(NC(=O)C(=CC1=CC=CO1)N1N=NN=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 11, 11, 5, 11, 1, 5, 5, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 15, 15, 15, 17, 17, 17, 17, 17, 15, 11, 5, 13, 13, 13, 4, 4, 4, 4, 4] 20 rigid atoms, others: [8, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918188 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918188 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918188/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918188 Building REAL300004918189 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918189' /scratch/stefan/7775246/working/building/REAL300004918189 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918189 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918189/0 /scratch/stefan/7775246/working/building/REAL300004918189 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/190 `/scratch/stefan/7775246/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004918189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918189 none CC#CCC(NC(=O)CSCC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 185, 149, 149, 80, 149, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 201, 201, 201, 201, 201, 185, 149, 80, 80, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 797 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918189 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918189 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918189/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918189 Building REAL300004918190 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918190' /scratch/stefan/7775246/working/building/REAL300004918190 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918190 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918190/0 /scratch/stefan/7775246/working/building/REAL300004918190 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/191 `/scratch/stefan/7775246/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918190 none CC#CCC(NC(=O)CSCC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 180, 143, 143, 68, 143, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 180, 184, 184, 201, 201, 201, 201, 201, 180, 143, 68, 68, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918190 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918190 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918190/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918190 Building REAL300004918191 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918191' /scratch/stefan/7775246/working/building/REAL300004918191 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918191 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918191/0 /scratch/stefan/7775246/working/building/REAL300004918191 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/192 `/scratch/stefan/7775246/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CSC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918191 none CC#CCC(NC(=O)C1=CC=C(CSC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 26, 49, 49, 49, 49, 49, 1, 1, 7, 11, 11, 24, 24, 24, 24, 24, 7, 3, 1, 1, 6, 6, 49, 49, 49, 49, 49, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 187 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918191 none CC#CCC(NC(=O)C1=CC=C(CSC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 76, 76, 41, 76, 21, 49, 49, 21, 5, 1, 1, 1, 1, 1, 1, 1, 49, 49, 122, 152, 152, 201, 201, 201, 201, 201, 122, 76, 49, 49, 21, 21, 1, 1, 1, 1, 1, 49, 49] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42]) total number of confs: 1053 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918191 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918191 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918191/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918191 Building REAL300004918192 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918192' /scratch/stefan/7775246/working/building/REAL300004918192 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918192 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918192/0 /scratch/stefan/7775246/working/building/REAL300004918192 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/193 `/scratch/stefan/7775246/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004918192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918192 none CC#CCC(NC(=O)C=CC1=CC=C(OCC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 26, 26, 5, 26, 5, 1, 1, 1, 1, 1, 1, 9, 24, 32, 39, 1, 1, 3, 1, 30, 30, 30, 40, 40, 40, 40, 40, 30, 26, 5, 5, 1, 1, 24, 24, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 49, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 347 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918192 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918192 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918192/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918192 Building REAL300004918193 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918193' /scratch/stefan/7775246/working/building/REAL300004918193 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918193 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918193/0 /scratch/stefan/7775246/working/building/REAL300004918193 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/194 `/scratch/stefan/7775246/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC)C(OCC)=C1)C(=O)[O-]) `REAL300004918193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918193 none CC#CCC(NC(=O)C=CC1=CC=C(OC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 40, 19, 19, 5, 19, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 9, 16, 1, 40, 56, 56, 81, 81, 81, 81, 81, 40, 19, 5, 5, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [33, 34, 43, 9, 10, 11, 12, 13, 14, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 459 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918193 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918193 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918193/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918193 Building REAL300004918194 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918194' /scratch/stefan/7775246/working/building/REAL300004918194 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918194 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918194/0 /scratch/stefan/7775246/working/building/REAL300004918194 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/195 `/scratch/stefan/7775246/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC2CC2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918194 none CC#CCC(NC(=O)C1=CC=C(NC2CC2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 25, 25, 1, 1, 2, 2, 1, 21, 39, 39, 90, 90, 90, 90, 90, 21, 7, 1, 1, 6, 25, 25, 25, 25, 25, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 472 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918194 none CC#CCC(NC(=O)C1=CC=C(NC2CC2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 63, 63, 9, 63, 9, 25, 25, 9, 1, 1, 1, 1, 25, 25, 25, 25, 25, 118, 150, 150, 201, 201, 201, 201, 201, 118, 63, 25, 25, 9, 1, 1, 1, 1, 1, 25] 201 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 966 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918194 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918194 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918194/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918194 Building REAL300004918195 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918195' /scratch/stefan/7775246/working/building/REAL300004918195 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918195 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918195/0 /scratch/stefan/7775246/working/building/REAL300004918195 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/196 `/scratch/stefan/7775246/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(CCC(C)C2)S1)C(=O)[O-]) `REAL300004918195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918195 none CC#CCC(NC(=O)C1=CC2=C(CCC(C)C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 35, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 47, 47, 68, 68, 68, 68, 68, 35, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 68 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918195 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918195 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918195/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918195 Building REAL300004918196 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918196' /scratch/stefan/7775246/working/building/REAL300004918196 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918196 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918196/0 /scratch/stefan/7775246/working/building/REAL300004918196 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/197 `/scratch/stefan/7775246/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C2OC3=C(CCCC3)C2=C1)C(=O)[O-]) `REAL300004918196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918196 none CC#CCC(NC(=O)COC1=CC=C2OC3=C(CCCC3)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 144, 93, 93, 23, 93, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 147, 147, 162, 162, 162, 162, 162, 144, 93, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 162 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 646 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918196 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918196 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918196/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918196 Building REAL300004918197 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918197' /scratch/stefan/7775246/working/building/REAL300004918197 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918197 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918197/0 /scratch/stefan/7775246/working/building/REAL300004918197 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/198 `/scratch/stefan/7775246/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)N1CCCCC1)C(=O)[O-]) `REAL300004918197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918197 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)N1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 13, 22, 22, 30, 30, 30, 30, 30, 13, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 63 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918197 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)N1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 19, 19, 11, 19, 11, 11, 11, 11, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 36, 50, 50, 63, 63, 63, 63, 63, 36, 19, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918197 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918197 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918197/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918197 Building REAL300004918198 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918198' /scratch/stefan/7775246/working/building/REAL300004918198 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918198 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918198/0 /scratch/stefan/7775246/working/building/REAL300004918198 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/199 `/scratch/stefan/7775246/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300004918198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918198 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 16, 15, 15, 11, 15, 11, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 20, 20, 20, 20, 20, 16, 15, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918198 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918198 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918198/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918198 Building REAL300004918199 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918199' /scratch/stefan/7775246/working/building/REAL300004918199 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918199 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918199/0 /scratch/stefan/7775246/working/building/REAL300004918199 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/200 `/scratch/stefan/7775246/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C)O1)C(=O)[O-]) `REAL300004918199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918199 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 37, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 13, 13, 13, 13, 13, 37, 62, 62, 107, 107, 107, 107, 107, 37, 12, 1, 4, 4, 3, 4, 4, 13, 13, 13, 13, 13] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918199 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 73, 73, 13, 73, 13, 13, 13, 13, 19, 19, 13, 19, 19, 13, 1, 1, 1, 1, 1, 1, 1, 128, 155, 155, 201, 201, 201, 201, 201, 128, 73, 13, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2] 201 rigid atoms, others: [41, 42, 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, 43, 44, 45]) total number of confs: 943 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918199 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 46, 20, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 46, 71, 71, 116, 116, 116, 116, 116, 46, 20, 4, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918199 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918199 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918199/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918199 Building REAL300004918200 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918200' /scratch/stefan/7775246/working/building/REAL300004918200 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918200 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918200/0 /scratch/stefan/7775246/working/building/REAL300004918200 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/201 `/scratch/stefan/7775246/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(Br)=CC=C2O1)C(=O)[O-]) `REAL300004918200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918200 none CC#CCC(NC(=O)C1=CC2=CC(Br)=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 38, 38, 57, 57, 57, 57, 57, 31, 12, 1, 1, 1, 1] 57 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918200 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918200 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918200/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918200 Building REAL300004918201 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918201' /scratch/stefan/7775246/working/building/REAL300004918201 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918201 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918201/0 /scratch/stefan/7775246/working/building/REAL300004918201 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/202 `/scratch/stefan/7775246/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2C=CC=N2)O1)C(=O)[O-]) `REAL300004918201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918201 none CC#CCC(NC(=O)C1=CC=C(CN2C=CC=N2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 1, 18, 28, 28, 46, 46, 46, 46, 46, 18, 6, 1, 1, 9, 9, 27, 27, 27] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918201 none CC#CCC(NC(=O)C1=CC=C(CN2C=CC=N2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 61, 61, 27, 61, 27, 27, 27, 8, 1, 1, 1, 1, 1, 1, 27, 118, 149, 149, 201, 201, 201, 201, 201, 118, 61, 27, 27, 8, 8, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 930 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918201 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918201 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918201/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918201 Building REAL300004918202 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918202' /scratch/stefan/7775246/working/building/REAL300004918202 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918202 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918202/0 /scratch/stefan/7775246/working/building/REAL300004918202 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/203 `/scratch/stefan/7775246/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C2=NC=CC=N2)C1)C(=O)[O-]) `REAL300004918202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918202 none CC#CCC(NC(=O)C1CCCN(C2=NC=CC=N2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 44, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 44, 74, 74, 137, 137, 137, 137, 137, 44, 13, 1, 1, 1, 1, 1, 1, 1, 7, 1, 7, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 40, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918202 none CC#CCC(NC(=O)C1CCCN(C2=NC=CC=N2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 76, 76, 11, 76, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 139, 161, 161, 201, 201, 201, 201, 201, 139, 76, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11] 201 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 860 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918202 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918202 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918202/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918202 Building REAL300004918203 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918203' /scratch/stefan/7775246/working/building/REAL300004918203 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918203 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918203/0 /scratch/stefan/7775246/working/building/REAL300004918203 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/204 `/scratch/stefan/7775246/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CNC2=CC=CC=C12)NC(=O)C(C)C)C(=O)[O-]) `REAL300004918203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918203 none CC#CCC(NC(=O)C(CC1=CNC2=CC=CC=C12)NC(=O)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 88, 53, 53, 16, 53, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 30, 30, 30, 68, 68, 88, 88, 88, 146, 146, 146, 146, 146, 88, 53, 16, 5, 5, 1, 1, 1, 1, 1, 1, 30, 68, 68, 68, 68, 68, 68, 68] 187 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918203 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918203 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918203/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918203 Building REAL300004918204 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918204' /scratch/stefan/7775246/working/building/REAL300004918204 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918204 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918204/0 /scratch/stefan/7775246/working/building/REAL300004918204 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/205 `/scratch/stefan/7775246/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)CC(C)C)C(C)C)C(=O)[O-]) `REAL300004918204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918204 none CC#CCC(NC(=O)C(NC(=O)CC(C)C)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 7, 7, 1, 7, 1, 1, 4, 4, 4, 8, 8, 8, 1, 5, 5, 11, 14, 14, 19, 19, 19, 19, 19, 11, 7, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 31 rigid atoms, others: [8, 9, 29, 6, 16] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918204 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918204 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918204/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918204 Building REAL300004918205 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918205' /scratch/stefan/7775246/working/building/REAL300004918205 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918205 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918205/0 /scratch/stefan/7775246/working/building/REAL300004918205 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/206 `/scratch/stefan/7775246/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=NC=CS2)C(C)=C1)C(=O)[O-]) `REAL300004918205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918205 none CC#CCC(NC(=O)C1=C(C)N(C2=NC=CS2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 8, 1, 1, 14, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 1, 36, 61, 61, 95, 95, 95, 95, 95, 36, 12, 2, 2, 2, 10, 10, 2, 2, 2, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 504 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918205 none CC#CCC(NC(=O)C1=C(C)N(C2=NC=CS2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 8, 1, 1, 14, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 58, 58, 10, 58, 10, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 10, 118, 150, 150, 201, 201, 201, 201, 201, 118, 58, 10, 10, 10, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 937 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918205 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918205 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918205/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918205 Building REAL300004918206 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918206' /scratch/stefan/7775246/working/building/REAL300004918206 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918206 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918206/0 /scratch/stefan/7775246/working/building/REAL300004918206 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/207 `/scratch/stefan/7775246/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC(C(C)C)=C1)C(=O)[O-]) `REAL300004918206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918206 none CC#CCC(NC(=O)COC1=CC=CC(C(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 149, 86, 86, 21, 86, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 149, 166, 166, 193, 193, 193, 193, 193, 149, 86, 21, 21, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 41, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 878 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918206 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918206 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918206/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918206 Building REAL300004918207 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918207' /scratch/stefan/7775246/working/building/REAL300004918207 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918207 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918207/0 /scratch/stefan/7775246/working/building/REAL300004918207 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/208 `/scratch/stefan/7775246/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC(C(C)C)=C1)C(=O)[O-]) `REAL300004918207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918207 none CC#CCC(NC(=O)C(C)OC1=CC=CC(C(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 116, 81, 81, 29, 81, 11, 29, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 116, 145, 145, 178, 178, 178, 178, 178, 116, 81, 29, 29, 29, 29, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [34, 35, 36, 44, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 927 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918207 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918207 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918207/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918207 Building REAL300004918208 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918208' /scratch/stefan/7775246/working/building/REAL300004918208 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918208 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918208/0 /scratch/stefan/7775246/working/building/REAL300004918208 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/209 `/scratch/stefan/7775246/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC(C)=CC=C1C(C)C)C(=O)[O-]) `REAL300004918208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918208 none CC#CCC(NC(=O)C(C)OC1=CC(C)=CC=C1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 67, 67, 15, 67, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 150, 150, 201, 201, 201, 201, 201, 105, 67, 15, 15, 15, 15, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [35, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 1050 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918208 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918208 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918208/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918208 Building REAL300004918209 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918209' /scratch/stefan/7775246/working/building/REAL300004918209 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918209 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918209/0 /scratch/stefan/7775246/working/building/REAL300004918209 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/210 `/scratch/stefan/7775246/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(C(C)C)C(C)=C1)C(=O)[O-]) `REAL300004918209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918209 none CC#CCC(NC(=O)C(C)OC1=CC=C(C(C)C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 164, 104, 104, 26, 104, 11, 26, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 164, 175, 175, 201, 201, 201, 201, 201, 164, 104, 26, 26, 26, 26, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [35, 36, 10, 11, 12, 13, 14, 15, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 873 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918209 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918209 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918209/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918209 Building REAL300004918210 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918210' /scratch/stefan/7775246/working/building/REAL300004918210 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918210 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918210/0 /scratch/stefan/7775246/working/building/REAL300004918210 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/211 `/scratch/stefan/7775246/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC2=CC=C(Br)C=C2C=C1)C(=O)[O-]) `REAL300004918210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918210 none CC#CCC(NC(=O)COC1=CC2=CC=C(Br)C=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 115, 78, 78, 21, 78, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 124, 124, 136, 136, 136, 136, 136, 115, 78, 21, 21, 1, 1, 1, 1, 1, 1] 136 rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 577 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918210 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918210 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918210/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918210 Building REAL300004918211 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918211' /scratch/stefan/7775246/working/building/REAL300004918211 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918211 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918211/0 /scratch/stefan/7775246/working/building/REAL300004918211 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/212 `/scratch/stefan/7775246/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(C2=NC(C)=CC(C)=N2)N=C1C)C(=O)[O-]) `REAL300004918211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918211 none CC#CCC(NC(=O)CC1=C(C)N(C2=NC(C)=CC(C)=N2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 53, 25, 25, 6, 25, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 3, 3, 3, 1, 1, 1, 53, 83, 83, 102, 102, 102, 102, 102, 53, 25, 6, 6, 2, 2, 2, 4, 4, 4, 1, 4, 4, 4, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 571 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918211 none CC#CCC(NC(=O)CC1=C(C)N(C2=NC(C)=CC(C)=N2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 71, 71, 19, 71, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 124, 153, 153, 201, 201, 201, 201, 201, 124, 71, 19, 19, 7, 7, 7, 2, 2, 2, 1, 2, 2, 2, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 987 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918211 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918211 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918211/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918211 Building REAL300004918212 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918212' /scratch/stefan/7775246/working/building/REAL300004918212 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918212 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918212/0 /scratch/stefan/7775246/working/building/REAL300004918212 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/213 `/scratch/stefan/7775246/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(C2=CC=C(Cl)C=C2)N=C1C)C(=O)[O-]) `REAL300004918212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918212 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=C(Cl)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 65, 28, 27, 6, 28, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 65, 106, 106, 159, 159, 159, 159, 159, 65, 27, 6, 6, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 828 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918212 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=C(Cl)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 52, 52, 12, 52, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 110, 147, 147, 201, 201, 201, 201, 201, 110, 52, 12, 12, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 988 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918212 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918212 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918212/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918212 Building REAL300004918213 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918213' /scratch/stefan/7775246/working/building/REAL300004918213 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918213 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918213/0 /scratch/stefan/7775246/working/building/REAL300004918213 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/214 `/scratch/stefan/7775246/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(C2=CC=C(F)C=C2)N=C1C)C(=O)[O-]) `REAL300004918213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918213 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=C(F)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 66, 28, 27, 6, 28, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 66, 106, 106, 158, 158, 158, 158, 158, 66, 27, 6, 6, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 818 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918213 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=C(F)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 52, 52, 12, 52, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 111, 147, 147, 201, 201, 201, 201, 201, 111, 52, 12, 12, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 981 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918213 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918213 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918213/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918213 Building REAL300004918214 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918214' /scratch/stefan/7775246/working/building/REAL300004918214 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918214 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918214/0 /scratch/stefan/7775246/working/building/REAL300004918214 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/215 `/scratch/stefan/7775246/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004918214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918214 none CC#CCC(NC(=O)C(C)SC1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 44, 32, 32, 14, 32, 6, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 48, 48, 54, 54, 54, 54, 54, 44, 32, 14, 14, 14, 14, 1, 1, 1, 1] 54 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918214 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918214 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918214/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918214 Building REAL300004918215 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918215' /scratch/stefan/7775246/working/building/REAL300004918215 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918215 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918215/0 /scratch/stefan/7775246/working/building/REAL300004918215 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/216 `/scratch/stefan/7775246/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(N)=O)C=C1)C(=O)[O-]) `REAL300004918215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918215 none CC#CCC(NC(=O)C1=CC=C(CNC(N)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 34, 34, 34, 1, 1, 9, 13, 13, 31, 31, 31, 31, 31, 9, 3, 1, 1, 6, 6, 34, 34, 34, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918215 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918215 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918215/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918215 Building REAL300004918216 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918216' /scratch/stefan/7775246/working/building/REAL300004918216 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918216 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918216/0 /scratch/stefan/7775246/working/building/REAL300004918216 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/217 `/scratch/stefan/7775246/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCCC)C(OCCC)=C1)C(=O)[O-]) `REAL300004918216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918216 none CC#CCC(NC(=O)C1=CC=C(OCCC)C(OCCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 20, 38, 1, 1, 9, 14, 30, 1, 6, 7, 7, 13, 13, 13, 13, 13, 6, 5, 1, 1, 20, 20, 39, 39, 39, 39, 39, 14, 14, 30, 30, 30, 30, 30, 1] 201 rigid atoms, others: [32, 33, 6, 48, 8, 9, 10, 11, 12, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918216 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918216 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918216/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918216 Building REAL300004918217 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918217' /scratch/stefan/7775246/working/building/REAL300004918217 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918217 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918217/0 /scratch/stefan/7775246/working/building/REAL300004918217 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/218 `/scratch/stefan/7775246/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(CCCC2=O)N1)C(=O)[O-]) `REAL300004918217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918217 none CC#CCC(NC(=O)C1=C(C)C2=C(CCCC2=O)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 5, 5, 5, 1, 11, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 36, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 49, 49, 71, 71, 71, 71, 71, 36, 13, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 340 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918217 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918217 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918217/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918217 Building REAL300004918218 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918218' /scratch/stefan/7775246/working/building/REAL300004918218 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918218 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918218/0 /scratch/stefan/7775246/working/building/REAL300004918218 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/219 `/scratch/stefan/7775246/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2CCCCC2)C=C1)C(=O)[O-]) `REAL300004918218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918218 none CC#CCC(NC(=O)C1=CC=C(C2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 13, 21, 21, 41, 41, 41, 41, 41, 13, 4, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 102 rigid atoms, others: [43, 6, 8, 9, 10, 11, 12, 44, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918218 none CC#CCC(NC(=O)C1=CC=C(C2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 52, 19, 19, 2, 19, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 64, 64, 102, 102, 102, 102, 102, 52, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 102 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918218 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918218 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918218/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918218 Building REAL300004918219 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918219' /scratch/stefan/7775246/working/building/REAL300004918219 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918219 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918219/0 /scratch/stefan/7775246/working/building/REAL300004918219 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/220 `/scratch/stefan/7775246/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C12CC3CC(CC(C3)C1)C2)C(C)C)C(=O)[O-]) `REAL300004918219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918219 none CC#CCC(NC(=O)C(NC(=O)C12CC3CC(CC(C3)C1)C2)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 51, 51, 36, 20, 20, 6, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 13, 36, 37, 37, 51, 51, 51, 51, 51, 36, 20, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14] 55 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 259 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918219 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918219 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918219/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918219 Building REAL300004918220 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918220' /scratch/stefan/7775246/working/building/REAL300004918220 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918220 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918220/0 /scratch/stefan/7775246/working/building/REAL300004918220 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/221 `/scratch/stefan/7775246/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(C(C)=O)=CC=C1OC)C(=O)[O-]) `REAL300004918220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918220 none CC#CCC(NC(=O)CC1=CC(C(C)=O)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 53, 24, 24, 6, 24, 1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 1, 3, 53, 82, 82, 124, 124, 124, 124, 124, 53, 24, 6, 6, 1, 9, 9, 9, 1, 1, 4, 4, 4] 201 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918220 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918220 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918220/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918220 Building REAL300004918221 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918221' /scratch/stefan/7775246/working/building/REAL300004918221 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918221 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918221/0 /scratch/stefan/7775246/working/building/REAL300004918221 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/222 `/scratch/stefan/7775246/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCN(C)S(=O)(=O)C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918221 none CC#CCC(NC(=O)CCCN(C)S(=O)(=O)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 6 rigid atoms, others: [42, 43, 44, 13, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918221 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918221 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918221/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918221 Building REAL300004918222 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918222' /scratch/stefan/7775246/working/building/REAL300004918222 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918222 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918222/0 /scratch/stefan/7775246/working/building/REAL300004918222 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/223 `/scratch/stefan/7775246/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=C(C)C(C)=C1)C(=O)[O-]) `REAL300004918222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918222 none CC#CCC(NC(=O)CCSC1=CC=C(C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 86, 86, 25, 86, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 180, 180, 201, 201, 201, 201, 201, 133, 86, 24, 24, 22, 22, 1, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [33, 34, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 1040 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918222 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918222 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918222/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918222 Building REAL300004918223 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918223' /scratch/stefan/7775246/working/building/REAL300004918223 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918223 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918223/0 /scratch/stefan/7775246/working/building/REAL300004918223 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/224 `/scratch/stefan/7775246/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC(F)F)C=C1OC(F)F)C(=O)[O-]) `REAL300004918223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918223 none CC#CCC(NC(=O)C=CC1=CC=C(OC(F)F)C=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 16, 16, 7, 16, 7, 1, 1, 1, 1, 1, 1, 10, 12, 12, 1, 1, 1, 5, 7, 7, 23, 28, 28, 45, 45, 45, 45, 45, 23, 16, 7, 7, 1, 1, 12, 1, 7] 201 rigid atoms, others: [36, 37, 39, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 40]) total number of confs: 253 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918223 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918223 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918223/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918223 Building REAL300004918224 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918224' /scratch/stefan/7775246/working/building/REAL300004918224 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918224 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918224/0 /scratch/stefan/7775246/working/building/REAL300004918224 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/225 `/scratch/stefan/7775246/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-]) `REAL300004918224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918224 none CC#CCC(NC(=O)C(C)OC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 93, 53, 53, 14, 53, 6, 14, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 93, 103, 103, 169, 169, 169, 169, 169, 93, 53, 14, 14, 14, 14, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 192 rigid atoms, others: [35, 36, 10, 11, 12, 13, 14, 15, 19, 20, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 778 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918224 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918224 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918224/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918224 Building REAL300004918225 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918225' /scratch/stefan/7775246/working/building/REAL300004918225 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918225 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918225/0 /scratch/stefan/7775246/working/building/REAL300004918225 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/226 `/scratch/stefan/7775246/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(F)=CC=C2S1)C(=O)[O-]) `REAL300004918225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918225 none CC#CCC(NC(=O)C1=CC2=CC(F)=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 44, 44, 64, 64, 64, 64, 64, 34, 12, 1, 1, 1, 1] 64 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918225 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918225 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918225/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918225 Building REAL300004918226 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918226' /scratch/stefan/7775246/working/building/REAL300004918226 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918226 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918226/0 /scratch/stefan/7775246/working/building/REAL300004918226 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/227 `/scratch/stefan/7775246/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)N1CC(=O)NC2=CC=CC=C21)C(=O)[O-]) `REAL300004918226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918226 none CC#CCC(NC(=O)CCC(=O)N1CC(=O)NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 41, 32, 32, 17, 32, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 48, 48, 54, 54, 54, 54, 54, 41, 32, 17, 17, 13, 13, 1, 1, 1, 1, 1, 1, 1] 54 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918226 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918226 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918226/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918226 Building REAL300004918227 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918227' /scratch/stefan/7775246/working/building/REAL300004918227 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918227 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918227/0 /scratch/stefan/7775246/working/building/REAL300004918227 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/228 `/scratch/stefan/7775246/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-]) `REAL300004918227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918227 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 54, 31, 31, 8, 31, 8, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 54, 69, 69, 92, 92, 92, 92, 92, 54, 31, 8, 8, 1, 1, 13, 13, 11, 13] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918227 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 83, 83, 31, 83, 31, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 132, 156, 156, 201, 201, 201, 201, 201, 132, 83, 31, 31, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 908 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918227 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918227 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918227/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918227 Building REAL300004918228 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918228' /scratch/stefan/7775246/working/building/REAL300004918228 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918228 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918228/0 /scratch/stefan/7775246/working/building/REAL300004918228 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/229 `/scratch/stefan/7775246/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-]) `REAL300004918228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918228 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 27, 43, 43, 72, 72, 72, 72, 72, 27, 10, 1, 1, 13, 13, 12, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918228 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 58, 58, 13, 58, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 123, 158, 158, 201, 201, 201, 201, 201, 123, 58, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918228 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918228 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918228/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918228 Building REAL300004918229 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918229' /scratch/stefan/7775246/working/building/REAL300004918229 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918229 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918229/0 /scratch/stefan/7775246/working/building/REAL300004918229 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/230 `/scratch/stefan/7775246/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(C)N2N=CN=C2N=C1C)C(=O)[O-]) `REAL300004918229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918229 none CC#CCC(NC(=O)CCC1=C(C)N2N=CN=C2N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 8, 1, 8, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 60, 19, 19, 3, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 68, 68, 83, 83, 83, 83, 83, 60, 19, 3, 3, 3, 3, 2, 2, 2, 1, 2, 2, 2] 83 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 390 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918229 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918229 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918229/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918229 Building REAL300004918230 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918230' /scratch/stefan/7775246/working/building/REAL300004918230 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918230 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918230/0 /scratch/stefan/7775246/working/building/REAL300004918230 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/231 `/scratch/stefan/7775246/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC2CC2)=C1)C(=O)[O-]) `REAL300004918230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918230 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 1, 16, 24, 24, 43, 43, 43, 43, 43, 16, 5, 1, 1, 1, 9, 22, 22, 22, 22, 22, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918230 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 62, 62, 22, 62, 22, 22, 22, 22, 13, 5, 13, 13, 1, 1, 1, 1, 22, 117, 153, 153, 201, 201, 201, 201, 201, 117, 62, 22, 22, 22, 5, 1, 1, 1, 1, 1, 22] 201 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 963 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918230 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918230 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918230/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918230 Building REAL300004918231 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918231' /scratch/stefan/7775246/working/building/REAL300004918231 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918231 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918231/0 /scratch/stefan/7775246/working/building/REAL300004918231 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/232 `/scratch/stefan/7775246/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CCSC)NS(=O)(=O)CC)C(=O)[O-]) `REAL300004918231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918231 none CC#CCC(NC(=O)C(CCSC)NS(=O)(=O)CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 8, 14, 11, 11, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 8, 5, 5, 1, 5, 1, 1, 5, 5, 10, 1, 4, 7, 7, 7, 9, 8, 10, 10, 12, 12, 12, 12, 12, 8, 5, 1, 5, 5, 5, 5, 10, 10, 10, 4, 9, 9, 9, 9, 9] 31 rigid atoms, others: [8, 9, 13, 6, 29] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 1 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918231 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918231 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918231/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918231 Building REAL300004918232 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918232' /scratch/stefan/7775246/working/building/REAL300004918232 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918232 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918232/0 /scratch/stefan/7775246/working/building/REAL300004918232 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/233 `/scratch/stefan/7775246/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C=C2Cl)=N1)C(=O)[O-]) `REAL300004918232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918232 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 31, 10, 9, 1, 9, 1, 1, 1, 1, 1, 10, 10, 1, 9, 10, 10, 10, 1, 31, 47, 47, 74, 74, 74, 74, 74, 31, 10, 1, 10, 10, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918232 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 55, 55, 10, 55, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 121, 157, 157, 201, 201, 201, 201, 201, 121, 55, 10, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918232 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918232 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918232/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918232 Building REAL300004918233 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918233' /scratch/stefan/7775246/working/building/REAL300004918233 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918233 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918233/0 /scratch/stefan/7775246/working/building/REAL300004918233 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/234 `/scratch/stefan/7775246/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(S(C)(=O)=O)C=C1)C(=O)[O-]) `REAL300004918233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918233 none CC#CCC(NC(=O)CCCOC1=CC=C(S(C)(=O)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 153, 113, 113, 33, 113, 16, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 154, 154, 154, 170, 170, 170, 170, 170, 154, 113, 34, 34, 15, 15, 5, 5, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [43, 38, 39, 44, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918233 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918233 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918233/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918233 Building REAL300004918234 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918234' /scratch/stefan/7775246/working/building/REAL300004918234 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918234 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918234/0 /scratch/stefan/7775246/working/building/REAL300004918234 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/235 `/scratch/stefan/7775246/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(OC1=CC=C(Cl)C=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918234 none CC#CCC(NC(=O)C(OC1=CC=C(Cl)C=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 110, 66, 66, 14, 66, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 26, 26, 15, 26, 26, 110, 146, 146, 187, 187, 187, 187, 187, 110, 66, 14, 1, 1, 1, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 976 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918234 none CC#CCC(NC(=O)C(OC1=CC=C(Cl)C=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 42, 20, 20, 4, 20, 1, 4, 10, 26, 26, 16, 26, 26, 26, 1, 1, 1, 1, 1, 1, 42, 65, 65, 95, 95, 95, 95, 95, 42, 20, 4, 26, 26, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 8, 41, 42, 17, 18, 19, 20, 21, 22, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 567 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918234 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918234 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918234/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918234 Building REAL300004918235 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918235' /scratch/stefan/7775246/working/building/REAL300004918235 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918235 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918235/0 /scratch/stefan/7775246/working/building/REAL300004918235 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/236 `/scratch/stefan/7775246/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CS(N)(=O)=O)=C1)C(=O)[O-]) `REAL300004918235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918235 none CC#CCC(NC(=O)C1=CC=CC(CS(N)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 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: [40, 40, 40, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 1, 14, 22, 22, 40, 40, 40, 40, 40, 14, 5, 1, 1, 1, 5, 5, 20, 20, 1] 167 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 262 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918235 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918235 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918235/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918235 Building REAL300004918236 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918236' /scratch/stefan/7775246/working/building/REAL300004918236 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918236 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918236/0 /scratch/stefan/7775246/working/building/REAL300004918236 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/237 `/scratch/stefan/7775246/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=C(Br)S1)C(=O)[O-]) `REAL300004918236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918236 none CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 8, 11, 11, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 42, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 42, 57, 57, 82, 82, 82, 82, 82, 42, 12, 1, 4, 4] 124 rigid atoms, others: [6, 8, 9, 10, 11, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918236 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918236 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918236/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918236 Building REAL300004918237 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918237' /scratch/stefan/7775246/working/building/REAL300004918237 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918237 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918237/0 /scratch/stefan/7775246/working/building/REAL300004918237 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/238 `/scratch/stefan/7775246/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2F)N=C1)C(=O)[O-]) `REAL300004918237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918237 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2F)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 24, 5, 5, 1, 5, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 1, 24, 40, 40, 82, 82, 82, 82, 82, 24, 5, 1, 10, 10, 2, 10, 1] 194 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918237 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2F)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 101, 35, 35, 10, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 101, 131, 131, 194, 194, 194, 194, 194, 101, 35, 10, 1, 1, 1, 1, 10] 194 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 898 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918237 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918237 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918237/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918237 Building REAL300004918238 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918238' /scratch/stefan/7775246/working/building/REAL300004918238 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918238 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918238/0 /scratch/stefan/7775246/working/building/REAL300004918238 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/239 `/scratch/stefan/7775246/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC(C(C)C)=NC=C1Cl)C(=O)[O-]) `REAL300004918238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918238 none CC#CCC(NC(=O)C1=NC(C(C)C)=NC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 5, 5, 5, 8, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 24, 7, 7, 1, 7, 1, 1, 1, 1, 13, 13, 1, 1, 1, 1, 24, 45, 45, 91, 91, 91, 91, 91, 24, 7, 13, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918238 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918238 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918238/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918238 Building REAL300004918239 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918239' /scratch/stefan/7775246/working/building/REAL300004918239 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918239 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918239/0 /scratch/stefan/7775246/working/building/REAL300004918239 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/240 `/scratch/stefan/7775246/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C(NS(C)(=O)=O)=C1)C(=O)[O-]) `REAL300004918239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918239 none CC#CCC(NC(=O)C1=CC=C(F)C(NS(C)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 14, 5, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 1, 15, 26, 26, 42, 42, 42, 42, 42, 15, 5, 1, 1, 9, 18, 18, 18, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 14, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918239 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918239 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918239/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918239 Building REAL300004918240 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918240' /scratch/stefan/7775246/working/building/REAL300004918240 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918240 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918240/0 /scratch/stefan/7775246/working/building/REAL300004918240 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/241 `/scratch/stefan/7775246/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC(C(C)=O)=C1)C(=O)[O-]) `REAL300004918240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918240 none CC#CCC(NC(=O)CCCOC1=CC=CC(C(C)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 150, 120, 120, 44, 120, 35, 16, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 150, 150, 150, 168, 168, 168, 168, 168, 150, 120, 44, 44, 35, 35, 16, 16, 1, 1, 1, 10, 10, 10, 1] 201 rigid atoms, others: [43, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 711 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918240 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918240 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918240/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918240 Building REAL300004918241 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918241' /scratch/stefan/7775246/working/building/REAL300004918241 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918241 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918241/0 /scratch/stefan/7775246/working/building/REAL300004918241 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/242 `/scratch/stefan/7775246/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(CCC(C)=O)C=C1)C(=O)[O-]) `REAL300004918241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918241 none CC#CCC(NC(=O)C(C)OC1=CC=C(CCC(C)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 5, 1, 5, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 30, 19, 19, 11, 19, 6, 11, 1, 1, 1, 1, 1, 1, 2, 6, 21, 21, 1, 1, 30, 47, 47, 60, 60, 60, 60, 60, 30, 19, 11, 11, 11, 11, 1, 1, 2, 2, 6, 6, 22, 22, 22, 1, 1] 201 rigid atoms, others: [45, 36, 37, 10, 11, 12, 13, 14, 15, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918241 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918241 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918241/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918241 Building REAL300004918242 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918242' /scratch/stefan/7775246/working/building/REAL300004918242 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918242 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918242/0 /scratch/stefan/7775246/working/building/REAL300004918242 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/243 `/scratch/stefan/7775246/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC(C(C)=O)=C1)C(=O)[O-]) `REAL300004918242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918242 none CC#CCC(NC(=O)C(C)OC1=CC=CC(C(C)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 137, 76, 76, 25, 76, 11, 25, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 137, 141, 141, 169, 169, 169, 169, 169, 137, 76, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 1] 201 rigid atoms, others: [34, 35, 36, 40, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 761 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918242 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918242 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918242/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918242 Building REAL300004918243 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918243' /scratch/stefan/7775246/working/building/REAL300004918243 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918243 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918243/0 /scratch/stefan/7775246/working/building/REAL300004918243 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/244 `/scratch/stefan/7775246/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)CCOC)C=C1)C(=O)[O-]) `REAL300004918243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918243 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)CCOC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 16, 20, 41, 1, 1, 9, 15, 15, 29, 29, 29, 29, 29, 9, 3, 1, 1, 16, 16, 20, 20, 41, 41, 41, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 40, 19, 20, 41, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918243 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918243 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918243/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918243 Building REAL300004918244 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918244' /scratch/stefan/7775246/working/building/REAL300004918244 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918244 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918244/0 /scratch/stefan/7775246/working/building/REAL300004918244 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/245 `/scratch/stefan/7775246/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=CC2=CC([N+](=O)[O-])=CC=C21)C(=O)[O-]) `REAL300004918244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918244 none CC#CCC(NC(=O)CN1C=CC2=CC([N+](=O)[O-])=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 46, 46, 8, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 141, 141, 201, 201, 201, 201, 201, 102, 46, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 979 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918244 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918244 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918244/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918244 Building REAL300004918245 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918245' /scratch/stefan/7775246/working/building/REAL300004918245 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918245 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918245/0 /scratch/stefan/7775246/working/building/REAL300004918245 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/246 `/scratch/stefan/7775246/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=CC=C1N1C(C)=CC=C1C)C(=O)[O-]) `REAL300004918245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918245 none CC#CCC(NC(=O)C1=CC(C)=CC=C1N1C(C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 26, 36, 36, 61, 61, 61, 61, 61, 26, 9, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 67 rigid atoms, others: [32, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 294 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918245 none CC#CCC(NC(=O)C1=CC(C)=CC=C1N1C(C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 32, 13, 13, 4, 13, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 32, 43, 43, 67, 67, 67, 67, 67, 32, 13, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 2, 2, 2] 67 rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 331 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918245 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918245 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918245/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918245 Building REAL300004918246 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918246' /scratch/stefan/7775246/working/building/REAL300004918246 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918246 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918246/0 /scratch/stefan/7775246/working/building/REAL300004918246 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/247 `/scratch/stefan/7775246/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=C3OCOC3=C2)=N1)C(=O)[O-]) `REAL300004918246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918246 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C3OCOC3=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 53, 33, 33, 8, 33, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 1, 53, 55, 55, 79, 79, 79, 79, 79, 53, 33, 8, 8, 1, 5, 5, 5, 5, 5] 114 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918246 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C3OCOC3=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 98, 73, 73, 21, 73, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 98, 99, 99, 114, 114, 114, 114, 114, 98, 73, 21, 21, 5, 1, 1, 1, 1, 1] 114 rigid atoms, others: [36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918246 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918246 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918246/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918246 Building REAL300004918247 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918247' /scratch/stefan/7775246/working/building/REAL300004918247 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918247 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918247/0 /scratch/stefan/7775246/working/building/REAL300004918247 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/248 `/scratch/stefan/7775246/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C=C1)C(=O)[O-]) `REAL300004918247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918247 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 26, 10, 10, 1, 10, 1, 1, 1, 1, 11, 11, 1, 11, 11, 11, 1, 1, 26, 42, 42, 74, 74, 74, 74, 74, 26, 10, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918247 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 99, 49, 49, 11, 49, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 99, 143, 143, 201, 201, 201, 201, 201, 99, 49, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 984 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918247 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918247 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918247/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918247 Building REAL300004918248 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918248' /scratch/stefan/7775246/working/building/REAL300004918248 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918248 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918248/0 /scratch/stefan/7775246/working/building/REAL300004918248 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/249 `/scratch/stefan/7775246/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2Cl)N=C1)C(=O)[O-]) `REAL300004918248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918248 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2Cl)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 20, 5, 5, 1, 5, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 1, 20, 35, 35, 64, 64, 64, 64, 64, 20, 5, 1, 10, 10, 1, 10, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918248 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2Cl)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 86, 30, 30, 10, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 86, 121, 121, 201, 201, 201, 201, 201, 86, 30, 10, 1, 1, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 949 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918248 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918248 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918248/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918248 Building REAL300004918249 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918249' /scratch/stefan/7775246/working/building/REAL300004918249 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918249 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918249/0 /scratch/stefan/7775246/working/building/REAL300004918249 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/250 `/scratch/stefan/7775246/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2Cl)N=N1)C(=O)[O-]) `REAL300004918249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918249 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2Cl)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 39, 12, 12, 1, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 1, 1, 39, 61, 61, 92, 92, 92, 92, 92, 39, 12, 1, 8, 8, 2, 8] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918249 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2Cl)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 111, 46, 46, 8, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 111, 148, 148, 201, 201, 201, 201, 201, 111, 46, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 949 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918249 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918249 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918249/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918249 Building REAL300004918250 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918250' /scratch/stefan/7775246/working/building/REAL300004918250 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918250 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918250/0 /scratch/stefan/7775246/working/building/REAL300004918250 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/251 `/scratch/stefan/7775246/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004918250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918250 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 30, 29, 29, 17, 29, 14, 8, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 30, 30, 30, 36, 36, 36, 36, 36, 30, 29, 17, 17, 14, 14, 8, 1, 1, 3, 3, 3, 3, 3, 3, 1] 48 rigid atoms, others: [39, 40, 11, 14, 15, 16, 17, 18, 20, 21, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918250 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918250 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918250/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918250 Building REAL300004918251 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918251' /scratch/stefan/7775246/working/building/REAL300004918251 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918251 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918251/0 /scratch/stefan/7775246/working/building/REAL300004918251 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/252 `/scratch/stefan/7775246/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918251 none CC#CCC(NC(=O)CCCNC(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 19, 17, 17, 14, 17, 14, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 22, 22, 22, 22, 22, 19, 17, 14, 14, 14, 14, 13, 13, 3, 1, 1, 1, 1, 1] 22 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918251 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918251 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918251/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918251 Building REAL300004918252 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918252' /scratch/stefan/7775246/working/building/REAL300004918252 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918252 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918252/0 /scratch/stefan/7775246/working/building/REAL300004918252 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/253 `/scratch/stefan/7775246/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C2OCCOC2=C1)C(=O)[O-]) `REAL300004918252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918252 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 117, 44, 44, 6, 44, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 144, 144, 197, 197, 197, 197, 197, 117, 44, 6, 6, 1, 1, 1, 1, 1, 1] 197 rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 876 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918252 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918252 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918252/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918252 Building REAL300004918253 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918253' /scratch/stefan/7775246/working/building/REAL300004918253 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918253 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918253/0 /scratch/stefan/7775246/working/building/REAL300004918253 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/254 `/scratch/stefan/7775246/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C2OCCOC2=C1)C(=O)[O-]) `REAL300004918253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918253 none CC#CCC(NC(=O)C1=CC(Cl)=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 37, 37, 66, 66, 66, 66, 66, 25, 7, 1, 1, 1, 1, 1, 1] 66 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918253 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918253 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918253/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918253 Building REAL300004918254 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918254' /scratch/stefan/7775246/working/building/REAL300004918254 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918254 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918254/0 /scratch/stefan/7775246/working/building/REAL300004918254 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/255 `/scratch/stefan/7775246/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2Cl)O1)C(=O)[O-]) `REAL300004918254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918254 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2Cl)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 32, 49, 49, 77, 77, 77, 77, 77, 32, 10, 1, 1, 10, 10, 1, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918254 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2Cl)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 58, 58, 10, 58, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 123, 151, 151, 201, 201, 201, 201, 201, 123, 58, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 894 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918254 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918254 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918254/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918254 Building REAL300004918255 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918255' /scratch/stefan/7775246/working/building/REAL300004918255 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918255 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918255/0 /scratch/stefan/7775246/working/building/REAL300004918255 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/256 `/scratch/stefan/7775246/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C2OCOC2=C1)C(=O)[O-]) `REAL300004918255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918255 none CC#CCC(NC(=O)C1=CC(Cl)=C2OCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 37, 37, 71, 71, 71, 71, 71, 25, 7, 1, 1, 1, 1] 71 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918255 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918255 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918255/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918255 Building REAL300004918256 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918256' /scratch/stefan/7775246/working/building/REAL300004918256 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918256 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918256/0 /scratch/stefan/7775246/working/building/REAL300004918256 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/257 `/scratch/stefan/7775246/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004918256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918256 none CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 30, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 30, 45, 45, 77, 77, 77, 77, 77, 30, 12, 1, 1, 1, 1, 24, 24, 24] 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]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918256 none CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 82, 82, 24, 82, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 122, 155, 155, 201, 201, 201, 201, 201, 122, 82, 24, 24, 24, 24, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 909 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918256 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918256 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918256/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918256 Building REAL300004918257 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918257' /scratch/stefan/7775246/working/building/REAL300004918257 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918257 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918257/0 /scratch/stefan/7775246/working/building/REAL300004918257 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/258 `/scratch/stefan/7775246/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=C(C)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004918257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918257 none CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=C(C)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 87, 56, 56, 9, 55, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 87, 88, 88, 107, 107, 107, 107, 107, 87, 56, 10, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1] 108 rigid atoms, others: [9, 10, 11, 12, 13, 14, 49, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918257 none CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=C(C)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 106, 83, 83, 19, 83, 19, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 106, 106, 106, 108, 108, 108, 108, 108, 106, 83, 19, 19, 3, 3, 3, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3] 108 rigid atoms, others: [45, 39, 40, 44, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918257 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918257 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918257/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918257 Building REAL300004918258 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918258' /scratch/stefan/7775246/working/building/REAL300004918258 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918258 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918258/0 /scratch/stefan/7775246/working/building/REAL300004918258 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/259 `/scratch/stefan/7775246/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)S1)C(=O)[O-]) `REAL300004918258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918258 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 40, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 40, 63, 63, 81, 81, 81, 81, 81, 40, 13, 1, 1, 6, 6, 6, 6] 148 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918258 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 103, 56, 56, 6, 56, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 103, 123, 123, 148, 148, 148, 148, 148, 103, 56, 6, 6, 1, 1, 1, 1] 148 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918258 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918258 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918258/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918258 Building REAL300004918259 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918259' /scratch/stefan/7775246/working/building/REAL300004918259 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918259 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918259/0 /scratch/stefan/7775246/working/building/REAL300004918259 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/260 `/scratch/stefan/7775246/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(CCCC)C=C1)C(=O)[O-]) `REAL300004918259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918259 none CC#CCC(NC(=O)CC1=CC=C(CCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 28, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 7, 11, 15, 1, 1, 28, 41, 41, 73, 73, 73, 73, 73, 28, 9, 3, 3, 1, 1, 7, 7, 11, 11, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 17, 18, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918259 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918259 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918259/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918259 Building REAL300004918260 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918260' /scratch/stefan/7775246/working/building/REAL300004918260 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918260 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918260/0 /scratch/stefan/7775246/working/building/REAL300004918260 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/261 `/scratch/stefan/7775246/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918260 none CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 2, 2, 1, 28, 42, 42, 80, 80, 80, 80, 80, 28, 7, 1, 1, 7, 7, 1] 150 rigid atoms, others: [32, 33, 36, 6, 8, 9, 10, 11, 12, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918260 none CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 81, 29, 29, 7, 29, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 81, 98, 98, 150, 150, 150, 150, 150, 81, 29, 7, 7, 1, 1, 7] 150 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918260 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918260 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918260/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918260 Building REAL300004918261 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918261' /scratch/stefan/7775246/working/building/REAL300004918261 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918261 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918261/0 /scratch/stefan/7775246/working/building/REAL300004918261 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/262 `/scratch/stefan/7775246/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)NC)C=C1)C(=O)[O-]) `REAL300004918261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918261 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)NC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 1, 1, 5, 7, 7, 15, 15, 15, 15, 15, 5, 3, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 18 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918261 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918261 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918261/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918261 Building REAL300004918262 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918262' /scratch/stefan/7775246/working/building/REAL300004918262 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918262 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918262/0 /scratch/stefan/7775246/working/building/REAL300004918262 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/263 `/scratch/stefan/7775246/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(C)C(S(N)(=O)=O)=C1)C(=O)[O-]) `REAL300004918262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918262 none CC#CCC(NC(=O)C1=CC(C)=C(C)C(S(N)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 5, 1, 14, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 26, 39, 39, 81, 81, 81, 81, 81, 26, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1] 81 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918262 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918262 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918262/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918262 Building REAL300004918263 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918263' /scratch/stefan/7775246/working/building/REAL300004918263 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918263 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918263/0 /scratch/stefan/7775246/working/building/REAL300004918263 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/264 `/scratch/stefan/7775246/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(C)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004918263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918263 none CC#CCC(NC(=O)C1=CC(C)=C(C)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 1, 30, 43, 43, 81, 81, 81, 81, 81, 30, 7, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1] 138 rigid atoms, others: [32, 45, 6, 8, 9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 383 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918263 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918263 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918263/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918263 Building REAL300004918264 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918264' /scratch/stefan/7775246/working/building/REAL300004918264 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918264 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918264/0 /scratch/stefan/7775246/working/building/REAL300004918264 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/265 `/scratch/stefan/7775246/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC(F)=CC=C2O1)C(=O)[O-]) `REAL300004918264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918264 none CC#CCC(NC(=O)C1=C(C)C2=CC(F)=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 41, 41, 58, 58, 58, 58, 58, 31, 12, 2, 2, 2, 1, 1, 1] 58 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 278 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918264 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918264 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918264/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918264 Building REAL300004918265 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918265' /scratch/stefan/7775246/working/building/REAL300004918265 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918265 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918265/0 /scratch/stefan/7775246/working/building/REAL300004918265 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/266 `/scratch/stefan/7775246/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC=CC(F)=C2O1)C(=O)[O-]) `REAL300004918265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918265 none CC#CCC(NC(=O)C1=C(C)C2=CC=CC(F)=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 47, 47, 62, 62, 62, 62, 62, 34, 11, 2, 2, 2, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 315 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918265 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918265 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918265/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918265 Building REAL300004918266 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918266' /scratch/stefan/7775246/working/building/REAL300004918266 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918266 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918266/0 /scratch/stefan/7775246/working/building/REAL300004918266 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/267 `/scratch/stefan/7775246/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCCO2)C(=O)[O-]) `REAL300004918266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918266 none CC#CCC(NC(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 2, 2, 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, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 15, 21, 21, 37, 37, 37, 37, 37, 15, 6, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918266 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918266 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918266/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918266 Building REAL300004918267 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918267' /scratch/stefan/7775246/working/building/REAL300004918267 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918267 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918267/0 /scratch/stefan/7775246/working/building/REAL300004918267 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/268 `/scratch/stefan/7775246/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN2CCS(=O)(=O)N=C2C=C1)C(=O)[O-]) `REAL300004918267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918267 none CC#CCC(NC(=O)C1=CN2CCS(=O)(=O)N=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 46, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 58, 58, 83, 83, 83, 83, 83, 46, 13, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918267 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918267 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918267/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918267 Building REAL300004918268 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918268' /scratch/stefan/7775246/working/building/REAL300004918268 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918268 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918268/0 /scratch/stefan/7775246/working/building/REAL300004918268 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/269 `/scratch/stefan/7775246/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=CC=C2)C(C)=C1)C(=O)[O-]) `REAL300004918268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918268 none CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 94, 52, 52, 9, 52, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 94, 134, 134, 157, 157, 157, 157, 157, 94, 53, 9, 9, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 792 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918268 none CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 81, 81, 19, 81, 19, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 134, 154, 154, 201, 201, 201, 201, 201, 134, 81, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [38, 39, 40, 41, 42, 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, 43, 44, 45, 46]) total number of confs: 894 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918268 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918268 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918268/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918268 Building REAL300004918269 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918269' /scratch/stefan/7775246/working/building/REAL300004918269 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918269 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918269/0 /scratch/stefan/7775246/working/building/REAL300004918269 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/270 `/scratch/stefan/7775246/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918269 none CC#CCC(NC(=O)C1=CC=C(NC(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 13, 21, 21, 1, 1, 9, 15, 15, 33, 33, 33, 33, 33, 9, 3, 1, 1, 11, 11, 21, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 44, 43, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918269 none CC#CCC(NC(=O)C1=CC=C(NC(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 101, 41, 41, 21, 41, 13, 21, 21, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 21, 21, 101, 135, 135, 201, 201, 201, 201, 201, 101, 41, 21, 21, 5, 3, 1, 1, 1, 1, 1, 21, 21] 201 rigid atoms, others: [38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 1014 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918269 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918269 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918269/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918269 Building REAL300004918270 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918270' /scratch/stefan/7775246/working/building/REAL300004918270 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918270 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918270/0 /scratch/stefan/7775246/working/building/REAL300004918270 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/271 `/scratch/stefan/7775246/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCC1=NC2=CC=CC=C2S1)C(=O)[O-]) `REAL300004918270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918270 none CC#CCC(NC(=O)CCCCC1=NC2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 132, 132, 36, 132, 15, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 201, 201, 201, 201, 201, 185, 132, 36, 36, 15, 15, 13, 13, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918270 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918270 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918270/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918270 Building REAL300004918271 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918271' /scratch/stefan/7775246/working/building/REAL300004918271 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918271 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918271/0 /scratch/stefan/7775246/working/building/REAL300004918271 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/272 `/scratch/stefan/7775246/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(OC)=C2OCCOC2=C1)C(=O)[O-]) `REAL300004918271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918271 none CC#CCC(NC(=O)C=CC1=CC(OC)=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 75, 31, 31, 6, 31, 6, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 75, 109, 109, 159, 159, 159, 159, 159, 75, 31, 6, 6, 1, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 38, 39, 40, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 762 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918271 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918271 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918271/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918271 Building REAL300004918272 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918272' /scratch/stefan/7775246/working/building/REAL300004918272 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918272 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918272/0 /scratch/stefan/7775246/working/building/REAL300004918272 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/273 `/scratch/stefan/7775246/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2[N+](=O)[O-])C(C)=CC1=O)C(=O)[O-]) `REAL300004918272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918272 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2[N+](=O)[O-])C(C)=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 64, 12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 64, 87, 87, 124, 124, 124, 124, 124, 64, 12, 3, 3, 1, 3, 2, 2, 2, 1] 183 rigid atoms, others: [6, 8, 9, 10, 11, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918272 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2[N+](=O)[O-])C(C)=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 102, 25, 25, 3, 25, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 102, 131, 131, 183, 183, 183, 183, 183, 102, 25, 1, 1, 1, 1, 3, 3, 3, 3] 183 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918272 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918272 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918272/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918272 Building REAL300004918273 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918273' /scratch/stefan/7775246/working/building/REAL300004918273 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918273 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918273/0 /scratch/stefan/7775246/working/building/REAL300004918273 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/274 `/scratch/stefan/7775246/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C2OCOC2=C1)C(=O)[O-]) `REAL300004918273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918273 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C2OCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 112, 45, 45, 6, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 112, 138, 138, 190, 190, 190, 190, 190, 112, 45, 7, 6, 1, 1, 1, 1] 190 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 837 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918273 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918273 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918273/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918273 Building REAL300004918274 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918274' /scratch/stefan/7775246/working/building/REAL300004918274 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918274 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918274/0 /scratch/stefan/7775246/working/building/REAL300004918274 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/275 `/scratch/stefan/7775246/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=CC=C1N1CCOCC1)C(=O)[O-]) `REAL300004918274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918274 none CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=CC=C1N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 31, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 31, 40, 40, 53, 53, 53, 53, 53, 31, 12, 1, 5, 5, 1, 1, 3, 3, 3, 4, 3, 4, 3, 3] 147 rigid atoms, others: [34, 37, 6, 8, 9, 10, 11, 15, 16, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 276 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918274 none CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=CC=C1N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 34, 16, 16, 4, 16, 3, 3, 3, 3, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 34, 43, 43, 53, 53, 53, 53, 53, 34, 16, 4, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 147 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 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]) total number of confs: 299 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918274 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918274 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918274/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918274 Building REAL300004918275 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918275' /scratch/stefan/7775246/working/building/REAL300004918275 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918275 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918275/0 /scratch/stefan/7775246/working/building/REAL300004918275 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/276 `/scratch/stefan/7775246/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)C2=CC=CS2)C=C1)C(=O)[O-]) `REAL300004918275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918275 none CC#CCC(NC(=O)C1=CC=C(NC(=O)C2=CC=CS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 9, 49, 49, 49, 49, 1, 1, 9, 15, 15, 39, 39, 39, 39, 39, 9, 3, 1, 1, 9, 49, 49, 49, 1, 1] 201 rigid atoms, others: [32, 33, 38, 6, 39, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918275 none CC#CCC(NC(=O)C1=CC=C(NC(=O)C2=CC=CS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 72, 72, 34, 72, 12, 49, 49, 11, 11, 1, 11, 1, 1, 1, 1, 1, 49, 49, 122, 146, 146, 201, 201, 201, 201, 201, 121, 72, 49, 49, 11, 1, 1, 1, 49, 49] 201 rigid atoms, others: [35, 36, 37, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 976 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918275 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918275 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918275/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918275 Building REAL300004918276 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918276' /scratch/stefan/7775246/working/building/REAL300004918276 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918276 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918276/0 /scratch/stefan/7775246/working/building/REAL300004918276 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/277 `/scratch/stefan/7775246/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)C2=CC=C(F)C=C2F)CC1)C(=O)[O-]) `REAL300004918276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918276 none CC#CCC(NC(=O)C1CCN(C(=O)C2=CC=C(F)C=C2F)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 7, 7, 14, 14, 12, 14, 14, 14, 14, 1, 1, 19, 28, 28, 40, 40, 40, 40, 40, 19, 10, 1, 1, 1, 1, 1, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 45, 44, 43, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918276 none CC#CCC(NC(=O)C1CCN(C(=O)C2=CC=C(F)C=C2F)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 68, 68, 14, 68, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 119, 162, 162, 201, 201, 201, 201, 201, 119, 68, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918276 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918276 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918276/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918276 Building REAL300004918277 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918277' /scratch/stefan/7775246/working/building/REAL300004918277 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918277 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918277/0 /scratch/stefan/7775246/working/building/REAL300004918277 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/278 `/scratch/stefan/7775246/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2NC(=O)COC2=C1)C(=O)[O-]) `REAL300004918277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918277 none CC#CCC(NC(=O)C1=CC=C2NC(=O)COC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 63, 63, 63, 63, 63, 26, 7, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918277 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918277 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918277/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918277 Building REAL300004918278 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918278' /scratch/stefan/7775246/working/building/REAL300004918278 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918278 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918278/0 /scratch/stefan/7775246/working/building/REAL300004918278 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/279 `/scratch/stefan/7775246/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C2CCCC2=C1)C(=O)[O-]) `REAL300004918278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918278 none CC#CCC(NC(=O)CSC1=CC=C2CCCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 157, 125, 125, 39, 125, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 157, 163, 163, 169, 169, 169, 169, 169, 157, 125, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 169 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 647 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918278 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918278 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918278/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918278 Building REAL300004918279 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918279' /scratch/stefan/7775246/working/building/REAL300004918279 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918279 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918279/0 /scratch/stefan/7775246/working/building/REAL300004918279 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/280 `/scratch/stefan/7775246/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918279 none CC#CCC(NC(=O)CCSC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 90, 90, 22, 90, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 128, 173, 173, 201, 201, 201, 201, 201, 128, 90, 22, 22, 19, 19, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 992 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918279 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918279 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918279/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918279 Building REAL300004918280 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918280' /scratch/stefan/7775246/working/building/REAL300004918280 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918280 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918280/0 /scratch/stefan/7775246/working/building/REAL300004918280 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/281 `/scratch/stefan/7775246/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(F)C=C1)C(C)C)C(=O)[O-]) `REAL300004918280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918280 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(F)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 27, 21, 21, 5, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 27, 27, 27, 31, 31, 31, 31, 31, 27, 21, 5, 3, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14] 34 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918280 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918280 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918280/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918280 Building REAL300004918281 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918281' /scratch/stefan/7775246/working/building/REAL300004918281 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918281 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918281/0 /scratch/stefan/7775246/working/building/REAL300004918281 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/282 `/scratch/stefan/7775246/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCCCC)C=C1)C(=O)[O-]) `REAL300004918281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918281 none CC#CCC(NC(=O)C1=CC=C(OCCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 11, 24, 33, 1, 1, 8, 13, 13, 26, 26, 26, 26, 26, 8, 3, 1, 1, 11, 11, 24, 24, 33, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 41, 40, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918281 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918281 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918281/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918281 Building REAL300004918282 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918282' /scratch/stefan/7775246/working/building/REAL300004918282 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918282 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918282/0 /scratch/stefan/7775246/working/building/REAL300004918282 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/283 `/scratch/stefan/7775246/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918282 none CC#CCC(NC(=O)CCSC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 157, 123, 123, 28, 123, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 157, 192, 192, 201, 201, 201, 201, 201, 157, 123, 28, 28, 27, 27, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 911 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918282 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918282 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918282/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918282 Building REAL300004918283 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918283' /scratch/stefan/7775246/working/building/REAL300004918283 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918283 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918283/0 /scratch/stefan/7775246/working/building/REAL300004918283 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/284 `/scratch/stefan/7775246/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)N2CCCCC2)S1)C(=O)[O-]) `REAL300004918283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918283 none CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)N2CCCCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 65, 37, 37, 7, 37, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 27, 27, 1, 65, 68, 68, 80, 80, 80, 80, 80, 65, 37, 7, 7, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918283 none CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)N2CCCCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 167, 167, 75, 167, 27, 27, 27, 27, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 27, 197, 199, 199, 201, 201, 201, 201, 201, 197, 167, 75, 75, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 13, 46, 45, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 737 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918283 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918283 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918283/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918283 Building REAL300004918284 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918284' /scratch/stefan/7775246/working/building/REAL300004918284 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918284 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918284/0 /scratch/stefan/7775246/working/building/REAL300004918284 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/285 `/scratch/stefan/7775246/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918284 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 22, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 9, 28, 52, 52, 52, 52, 52, 52, 22, 34, 34, 60, 60, 60, 60, 60, 22, 11, 1, 1, 1, 1, 28, 28, 52, 52, 52, 52] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918284 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 93, 93, 52, 93, 52, 52, 52, 52, 52, 18, 3, 1, 1, 1, 1, 1, 1, 1, 1, 131, 157, 157, 201, 201, 201, 201, 201, 131, 93, 52, 52, 52, 52, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 867 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918284 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918284 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918284/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918284 Building REAL300004918285 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918285' /scratch/stefan/7775246/working/building/REAL300004918285 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918285 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918285/0 /scratch/stefan/7775246/working/building/REAL300004918285 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/286 `/scratch/stefan/7775246/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918285 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 9, 26, 51, 51, 29, 51, 51, 51, 24, 36, 36, 53, 53, 53, 53, 53, 24, 11, 1, 1, 1, 1, 26, 26, 51, 51, 50, 51] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918285 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 132, 93, 93, 51, 93, 51, 51, 51, 51, 51, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 132, 155, 155, 201, 201, 201, 201, 201, 132, 93, 51, 51, 51, 51, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 905 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918285 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918285 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918285/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918285 Building REAL300004918286 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918286' /scratch/stefan/7775246/working/building/REAL300004918286 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918286 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918286/0 /scratch/stefan/7775246/working/building/REAL300004918286 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/287 `/scratch/stefan/7775246/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=C(Cl)C=C(Cl)C=C2S1)C(=O)[O-]) `REAL300004918286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918286 none CC#CCC(NC(=O)C1=C(Cl)C2=C(Cl)C=C(Cl)C=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 63, 63, 63, 63, 63, 26, 7, 1, 1] 63 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918286 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918286 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918286/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918286 Building REAL300004918287 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918287' /scratch/stefan/7775246/working/building/REAL300004918287 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918287 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918287/0 /scratch/stefan/7775246/working/building/REAL300004918287 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/288 `/scratch/stefan/7775246/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918287 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 22, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 9, 27, 50, 50, 27, 50, 50, 50, 22, 34, 34, 60, 60, 60, 60, 60, 22, 11, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918287 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 90, 90, 50, 90, 50, 50, 50, 50, 50, 18, 3, 1, 1, 1, 1, 1, 1, 1, 1, 130, 157, 157, 201, 201, 201, 201, 201, 130, 90, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918287 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918287 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918287/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918287 Building REAL300004918288 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918288' /scratch/stefan/7775246/working/building/REAL300004918288 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918288 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918288/0 /scratch/stefan/7775246/working/building/REAL300004918288 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/289 `/scratch/stefan/7775246/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918288 none CC#CCC(NC(=O)COC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 82, 82, 17, 82, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 121, 162, 162, 201, 201, 201, 201, 201, 121, 82, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1015 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918288 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918288 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918288/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918288 Building REAL300004918289 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918289' /scratch/stefan/7775246/working/building/REAL300004918289 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918289 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918289/0 /scratch/stefan/7775246/working/building/REAL300004918289 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/290 `/scratch/stefan/7775246/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918289 none CC#CCC(NC(=O)COC1=CC=CC=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 121, 78, 78, 24, 78, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 121, 125, 125, 145, 145, 145, 145, 145, 121, 78, 24, 24, 1, 1, 1, 1, 4, 4, 2, 4, 4] 145 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918289 none CC#CCC(NC(=O)COC1=CC=CC=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 133, 103, 103, 46, 103, 18, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 133, 135, 135, 145, 145, 145, 145, 145, 133, 103, 46, 46, 4, 4, 4, 4, 1, 1, 1, 1, 1] 145 rigid atoms, others: [38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918289 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918289 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918289/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918289 Building REAL300004918290 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918290' /scratch/stefan/7775246/working/building/REAL300004918290 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918290 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918290/0 /scratch/stefan/7775246/working/building/REAL300004918290 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/291 `/scratch/stefan/7775246/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCCOC1=CC=CC=C1)C(=O)[O-]) `REAL300004918290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918290 none CC#CCC(NC(=O)C1=CC=CC=C1OCCOC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 20, 23, 53, 63, 63, 53, 63, 63, 13, 21, 21, 39, 39, 39, 39, 39, 13, 5, 1, 1, 1, 1, 20, 20, 23, 23, 63, 63, 53, 63, 63] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918290 none CC#CCC(NC(=O)C1=CC=CC=C1OCCOC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 138, 92, 92, 63, 92, 63, 63, 63, 63, 63, 34, 11, 6, 4, 1, 1, 1, 1, 1, 1, 1, 138, 153, 153, 201, 201, 201, 201, 201, 138, 92, 63, 63, 63, 63, 11, 11, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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]) total number of confs: 858 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918290 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918290 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918290/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918290 Building REAL300004918291 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918291' /scratch/stefan/7775246/working/building/REAL300004918291 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918291 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918291/0 /scratch/stefan/7775246/working/building/REAL300004918291 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/292 `/scratch/stefan/7775246/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC(C)=CC=C1C(C)C)C(=O)[O-]) `REAL300004918291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918291 none CC#CCC(NC(=O)COC1=CC(C)=CC=C1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 95, 95, 26, 95, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 162, 162, 201, 201, 201, 201, 201, 131, 95, 26, 26, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 42, 43, 44]) total number of confs: 980 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918291 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918291 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918291/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918291 Building REAL300004918292 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918292' /scratch/stefan/7775246/working/building/REAL300004918292 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918292 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918292/0 /scratch/stefan/7775246/working/building/REAL300004918292 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/293 `/scratch/stefan/7775246/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C(NC(=O)C2=CC=CS2)=C1)C(=O)[O-]) `REAL300004918292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918292 none CC#CCC(NC(=O)C1=CC=C(Cl)C(NC(=O)C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 1, 17, 29, 29, 70, 70, 70, 70, 70, 17, 5, 1, 1, 9, 17, 17, 17, 1] 201 rigid atoms, others: [33, 34, 6, 39, 8, 9, 10, 11, 12, 13, 14, 22] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918292 none CC#CCC(NC(=O)C1=CC=C(Cl)C(NC(=O)C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 51, 51, 17, 51, 17, 17, 17, 17, 17, 6, 5, 1, 5, 1, 1, 1, 1, 1, 17, 98, 134, 134, 201, 201, 201, 201, 201, 98, 51, 17, 17, 6, 1, 1, 1, 17] 201 rigid atoms, others: [36, 37, 38, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918292 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918292 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918292/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918292 Building REAL300004918293 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918293' /scratch/stefan/7775246/working/building/REAL300004918293 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918293 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918293/0 /scratch/stefan/7775246/working/building/REAL300004918293 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/294 `/scratch/stefan/7775246/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918293 none CC#CCC(NC(=O)COC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 47, 32, 32, 8, 32, 3, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 47, 68, 68, 112, 112, 112, 112, 112, 47, 32, 8, 8, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 45, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918293 none CC#CCC(NC(=O)COC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 125, 125, 42, 125, 18, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 146, 172, 172, 201, 201, 201, 201, 201, 146, 125, 42, 42, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918293 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918293 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918293/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918293 Building REAL300004918294 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918294' /scratch/stefan/7775246/working/building/REAL300004918294 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918294 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918294/0 /scratch/stefan/7775246/working/building/REAL300004918294 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/295 `/scratch/stefan/7775246/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918294 none CC#CCC(NC(=O)CCSC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 88, 88, 21, 88, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 127, 172, 172, 201, 201, 201, 201, 201, 127, 88, 21, 21, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 983 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918294 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918294 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918294/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918294 Building REAL300004918295 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918295' /scratch/stefan/7775246/working/building/REAL300004918295 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918295 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918295/0 /scratch/stefan/7775246/working/building/REAL300004918295 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/296 `/scratch/stefan/7775246/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CO1)C(=O)[O-]) `REAL300004918295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918295 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 55, 28, 28, 7, 28, 2, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 18, 18, 18, 18, 55, 80, 80, 103, 103, 103, 103, 103, 55, 28, 7, 2, 2, 1, 1, 1, 1, 1, 16, 18, 18, 18] 148 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 571 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918295 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 63, 35, 35, 6, 35, 2, 6, 17, 18, 18, 17, 18, 18, 2, 1, 2, 1, 1, 1, 1, 1, 63, 88, 88, 111, 111, 111, 111, 111, 63, 35, 6, 17, 17, 18, 18, 18, 18, 18, 2, 1, 1, 1] 148 rigid atoms, others: [43, 44, 45, 17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 614 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918295 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918295 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918295/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918295 Building REAL300004918296 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918296' /scratch/stefan/7775246/working/building/REAL300004918296 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918296 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918296/0 /scratch/stefan/7775246/working/building/REAL300004918296 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/297 `/scratch/stefan/7775246/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004918296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918296 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 55, 27, 27, 7, 27, 2, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 24, 24, 24, 24, 55, 81, 81, 107, 107, 107, 107, 107, 55, 27, 7, 2, 2, 1, 1, 1, 1, 1, 16, 24, 24, 24] 154 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 592 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918296 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 69, 41, 41, 12, 41, 7, 12, 23, 24, 24, 23, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 69, 97, 97, 118, 118, 118, 118, 118, 69, 41, 12, 23, 23, 24, 24, 24, 24, 24, 7, 1, 1, 1] 154 rigid atoms, others: [43, 44, 45, 17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 654 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918296 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918296 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918296/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918296 Building REAL300004918297 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918297' /scratch/stefan/7775246/working/building/REAL300004918297 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918297 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918297/0 /scratch/stefan/7775246/working/building/REAL300004918297 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/298 `/scratch/stefan/7775246/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918297 none CC#CCC(NC(=O)COC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 66, 66, 14, 66, 4, 1, 1, 1, 1, 1, 1, 1, 1, 116, 153, 153, 201, 201, 201, 201, 201, 116, 66, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 971 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918297 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918297 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918297/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918297 Building REAL300004918298 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918298' /scratch/stefan/7775246/working/building/REAL300004918298 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918298 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918298/0 /scratch/stefan/7775246/working/building/REAL300004918298 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/299 `/scratch/stefan/7775246/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=NC3=CC=CC=C3S2)S1)C(=O)[O-]) `REAL300004918298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918298 none CC#CCC(NC(=O)C1=CC=C(C2=NC3=CC=CC=C3S2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 36, 13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 36, 57, 57, 96, 96, 96, 96, 96, 36, 13, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918298 none CC#CCC(NC(=O)C1=CC=C(C2=NC3=CC=CC=C3S2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 77, 77, 12, 77, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 133, 157, 157, 201, 201, 201, 201, 201, 133, 77, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 866 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918298 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918298 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918298/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918298 Building REAL300004918299 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918299' /scratch/stefan/7775246/working/building/REAL300004918299 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918299 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918299/0 /scratch/stefan/7775246/working/building/REAL300004918299 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/300 `/scratch/stefan/7775246/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(=CC1=CC=CC=C1OC)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918299 none CC#CCC(NC(=O)C(=CC1=CC=CC=C1OC)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 92, 42, 42, 6, 42, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 6, 7, 7, 92, 131, 131, 174, 174, 174, 174, 174, 92, 42, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7] 201 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 891 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918299 none CC#CCC(NC(=O)C(=CC1=CC=CC=C1OC)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 60, 27, 27, 4, 27, 1, 4, 4, 7, 7, 6, 7, 7, 7, 12, 1, 1, 1, 1, 1, 1, 60, 90, 90, 125, 125, 125, 125, 125, 60, 27, 4, 7, 7, 7, 7, 12, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918299 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918299 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918299/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918299 Building REAL300004918300 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918300' /scratch/stefan/7775246/working/building/REAL300004918300 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918300 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918300/0 /scratch/stefan/7775246/working/building/REAL300004918300 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/301 `/scratch/stefan/7775246/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1)C(=O)[O-]) `REAL300004918300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918300 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 1, 1, 16, 26, 26, 55, 55, 55, 55, 55, 16, 4, 1, 1, 22, 22, 22, 22, 22, 22, 1, 1] 157 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918300 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918300 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918300/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918300 Building REAL300004918301 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918301' /scratch/stefan/7775246/working/building/REAL300004918301 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918301 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918301/0 /scratch/stefan/7775246/working/building/REAL300004918301 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/302 `/scratch/stefan/7775246/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CO2)=C1)C(=O)[O-]) `REAL300004918301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918301 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 1, 17, 31, 31, 74, 74, 74, 74, 74, 17, 5, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 364 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918301 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 50, 50, 17, 50, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 17, 117, 153, 153, 201, 201, 201, 201, 201, 117, 50, 17, 17, 17, 17, 17, 5, 1, 1, 1, 17] 201 rigid atoms, others: [39, 40, 41, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42]) total number of confs: 948 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918301 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918301 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918301/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918301 Building REAL300004918302 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918302' /scratch/stefan/7775246/working/building/REAL300004918302 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918302 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918302/0 /scratch/stefan/7775246/working/building/REAL300004918302 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/303 `/scratch/stefan/7775246/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)N=C1C)C(=O)[O-]) `REAL300004918302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918302 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 59, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 59, 88, 88, 150, 150, 150, 150, 150, 59, 12, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2] 176 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 712 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918302 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 90, 26, 26, 4, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 90, 126, 126, 176, 176, 176, 176, 176, 90, 26, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4] 176 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 857 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918302 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918302 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918302/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918302 Building REAL300004918303 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918303' /scratch/stefan/7775246/working/building/REAL300004918303 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918303 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918303/0 /scratch/stefan/7775246/working/building/REAL300004918303 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/304 `/scratch/stefan/7775246/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C2OCCOC2=C1)C(=O)[O-]) `REAL300004918303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918303 none CC#CCC(NC(=O)C1=CC(OC)=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 31, 7, 7, 1, 7, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 31, 51, 51, 110, 110, 110, 110, 110, 31, 7, 1, 4, 4, 4, 1, 1, 1, 1, 1] 147 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 38, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 12, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918303 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918303 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918303/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918303 Building REAL300004918304 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918304' /scratch/stefan/7775246/working/building/REAL300004918304 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918304 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918304/0 /scratch/stefan/7775246/working/building/REAL300004918304 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/305 `/scratch/stefan/7775246/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CO2)C(C)=C1)C(=O)[O-]) `REAL300004918304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918304 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CO2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 1, 1, 1, 19, 28, 28, 47, 47, 47, 47, 47, 19, 9, 2, 2, 2, 2, 2, 9, 9, 9, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 250 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918304 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CO2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 54, 54, 9, 54, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 101, 140, 140, 201, 201, 201, 201, 201, 101, 54, 9, 9, 9, 5, 5, 1, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 976 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918304 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918304 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918304/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918304 Building REAL300004918305 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918305' /scratch/stefan/7775246/working/building/REAL300004918305 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918305 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918305/0 /scratch/stefan/7775246/working/building/REAL300004918305 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/306 `/scratch/stefan/7775246/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)C(C)=C1)C(=O)[O-]) `REAL300004918305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918305 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 5, 11, 11, 6, 11, 11, 1, 1, 1, 29, 48, 48, 63, 63, 63, 63, 63, 29, 10, 2, 2, 2, 5, 5, 11, 11, 11, 11, 11, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 45, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 382 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918305 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 63, 63, 11, 63, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 124, 156, 156, 201, 201, 201, 201, 201, 124, 63, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 939 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918305 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918305 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918305/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918305 Building REAL300004918306 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918306' /scratch/stefan/7775246/working/building/REAL300004918306 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918306 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918306/0 /scratch/stefan/7775246/working/building/REAL300004918306 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/307 `/scratch/stefan/7775246/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(C2SCCCS2)C=C1)C(=O)[O-]) `REAL300004918306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918306 none CC#CCC(NC(=O)COC1=CC=C(C2SCCCS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 14, 5, 5, 5, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 99, 62, 62, 13, 62, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 99, 105, 105, 132, 132, 132, 132, 132, 99, 62, 13, 13, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 44, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 593 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918306 none CC#CCC(NC(=O)COC1=CC=C(C2SCCCS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 14, 5, 5, 5, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 114, 114, 30, 114, 8, 2, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 163, 173, 173, 201, 201, 201, 201, 201, 163, 114, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 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, 43, 44]) total number of confs: 864 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918306 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918306 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918306/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918306 Building REAL300004918307 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918307' /scratch/stefan/7775246/working/building/REAL300004918307 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918307 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918307/0 /scratch/stefan/7775246/working/building/REAL300004918307 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/308 `/scratch/stefan/7775246/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)CCN2S(C)(=O)=O)C(=O)[O-]) `REAL300004918307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918307 none CC#CCC(NC(=O)C1=CC=C2C(=C1)CCN2S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 47, 47, 81, 81, 81, 81, 81, 28, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 194 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918307 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918307 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918307/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918307 Building REAL300004918308 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918308' /scratch/stefan/7775246/working/building/REAL300004918308 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918308 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918308/0 /scratch/stefan/7775246/working/building/REAL300004918308 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/309 `/scratch/stefan/7775246/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)CCCN2S(C)(=O)=O)C(=O)[O-]) `REAL300004918308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918308 none CC#CCC(NC(=O)C1=CC=C2C(=C1)CCCN2S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 27, 36, 36, 66, 66, 66, 66, 66, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3] 104 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918308 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918308 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918308/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918308 Building REAL300004918309 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918309' /scratch/stefan/7775246/working/building/REAL300004918309 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918309 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918309/0 /scratch/stefan/7775246/working/building/REAL300004918309 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/310 `/scratch/stefan/7775246/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC(Cl)=C1)C(=O)[O-]) `REAL300004918309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918309 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 5, 9, 9, 9, 21, 29, 29, 43, 43, 43, 43, 43, 21, 9, 1, 1, 1, 1, 1, 1, 1, 9, 5, 9] 81 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 231 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918309 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 49, 28, 28, 9, 28, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 49, 62, 62, 81, 81, 81, 81, 81, 49, 28, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 81 rigid atoms, others: [40, 41, 42, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 393 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918309 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918309 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918309/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918309 Building REAL300004918310 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918310' /scratch/stefan/7775246/working/building/REAL300004918310 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918310 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918310/0 /scratch/stefan/7775246/working/building/REAL300004918310 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/311 `/scratch/stefan/7775246/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1N(C)C(=O)C1CC1)C(=O)[O-]) `REAL300004918310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918310 none CC#CCC(NC(=O)C1=CC=CC=C1N(C)C(=O)C1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 4, 6, 6, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6] 9 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, 40, 41, 42]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918310 none CC#CCC(NC(=O)C1=CC=CC=C1N(C)C(=O)C1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 9 rigid atoms, others: [38, 39, 40, 41, 42, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918310 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918310 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918310/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918310 Building REAL300004918311 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918311' /scratch/stefan/7775246/working/building/REAL300004918311 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918311 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918311/0 /scratch/stefan/7775246/working/building/REAL300004918311 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/312 `/scratch/stefan/7775246/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC(C)=CC(C)=C2)C1)C(=O)[O-]) `REAL300004918311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918311 none CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC(C)=CC(C)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 32, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 1, 32, 52, 52, 77, 77, 77, 77, 77, 32, 13, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 50, 51, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 403 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918311 none CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC(C)=CC(C)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 81, 81, 20, 81, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 20, 145, 172, 172, 201, 201, 201, 201, 201, 145, 81, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 1, 2, 2, 2, 1, 20, 20] 201 rigid atoms, others: [45, 49, 41, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 46, 47, 48, 50, 51]) total number of confs: 931 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918311 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918311 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918311/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918311 Building REAL300004918312 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918312' /scratch/stefan/7775246/working/building/REAL300004918312 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918312 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918312/0 /scratch/stefan/7775246/working/building/REAL300004918312 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/313 `/scratch/stefan/7775246/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CC=C2F)=C1)C(=O)[O-]) `REAL300004918312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918312 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CC=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 9, 21, 21, 21, 1, 17, 31, 31, 60, 60, 60, 60, 60, 17, 5, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 1] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 45, 24] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 370 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918312 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CC=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 59, 59, 21, 59, 21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 21, 118, 147, 147, 201, 201, 201, 201, 201, 118, 59, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 21] 201 rigid atoms, others: [41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45]) total number of confs: 937 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918312 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918312 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918312/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918312 Building REAL300004918313 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918313' /scratch/stefan/7775246/working/building/REAL300004918313 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918313 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918313/0 /scratch/stefan/7775246/working/building/REAL300004918313 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/314 `/scratch/stefan/7775246/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918313 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 9, 15, 15, 1, 17, 32, 32, 63, 63, 63, 63, 63, 17, 5, 1, 1, 2, 2, 2, 9, 15, 15, 9, 15, 15, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 45, 23] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 350 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918313 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 48, 48, 15, 48, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 111, 145, 145, 201, 201, 201, 201, 201, 111, 48, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 15] 201 rigid atoms, others: [40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 972 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918313 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918313 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918313/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918313 Building REAL300004918314 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918314' /scratch/stefan/7775246/working/building/REAL300004918314 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918314 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918314/0 /scratch/stefan/7775246/working/building/REAL300004918314 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/315 `/scratch/stefan/7775246/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(NC(C)=O)=C1)C(=O)[O-]) `REAL300004918314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918314 none CC#CCC(NC(=O)C1=CC=C(C)C(NC(C)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 1, 5, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 29, 43, 43, 90, 90, 90, 90, 90, 29, 7, 1, 1, 2, 2, 2, 3, 3, 3, 3, 1] 151 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 14, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918314 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918314 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918314/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918314 Building REAL300004918315 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918315' /scratch/stefan/7775246/working/building/REAL300004918315 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918315 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918315/0 /scratch/stefan/7775246/working/building/REAL300004918315 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/316 `/scratch/stefan/7775246/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(S(=O)(=O)CCCC)CC1)C(=O)[O-]) `REAL300004918315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918315 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)CCCC)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 4, 4, 4, 14, 16, 20, 1, 1, 29, 44, 44, 71, 71, 71, 71, 71, 29, 11, 1, 1, 1, 1, 1, 14, 14, 16, 16, 20, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 46, 47, 48, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918315 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918315 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918315/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918315 Building REAL300004918316 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918316' /scratch/stefan/7775246/working/building/REAL300004918316 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918316 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918316/0 /scratch/stefan/7775246/working/building/REAL300004918316 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/317 `/scratch/stefan/7775246/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004918316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918316 none CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 19, 12, 12, 9, 12, 9, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 19, 19, 19, 24, 24, 24, 24, 24, 19, 12, 9, 9, 9, 9, 9, 1, 1, 1] 24 rigid atoms, others: [34, 35, 36, 11, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918316 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918316 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918316/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918316 Building REAL300004918317 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918317' /scratch/stefan/7775246/working/building/REAL300004918317 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918317 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918317/0 /scratch/stefan/7775246/working/building/REAL300004918317 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/318 `/scratch/stefan/7775246/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCN1S(=O)(=O)CCC)C(=O)[O-]) `REAL300004918317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918317 none CC#CCC(NC(=O)C1CCCCN1S(=O)(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 10, 11, 16, 16, 28, 28, 28, 28, 28, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10] 36 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918317 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918317 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918317/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918317 Building REAL300004918318 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918318' /scratch/stefan/7775246/working/building/REAL300004918318 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918318 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918318/0 /scratch/stefan/7775246/working/building/REAL300004918318 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/319 `/scratch/stefan/7775246/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNS(=O)(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004918318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918318 none CC#CCC(NC(=O)CNS(=O)(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1] 6 rigid atoms, others: [32, 33, 10, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918318 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918318 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918318/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918318 Building REAL300004918319 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918319' /scratch/stefan/7775246/working/building/REAL300004918319 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918319 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918319/0 /scratch/stefan/7775246/working/building/REAL300004918319 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/320 `/scratch/stefan/7775246/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1[N-]S(=O)(=O)CC)C(=O)[O-]) `REAL300004918319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918319 none CC#CCC(NC(=O)C1=CC=CC=C1[N-]S(=O)(=O)CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 4, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3] 8 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918319 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918319 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918319/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918319 Building REAL300004918320 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918320' /scratch/stefan/7775246/working/building/REAL300004918320 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918320 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918320/0 /scratch/stefan/7775246/working/building/REAL300004918320 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/321 `/scratch/stefan/7775246/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1S(=O)(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918320 none CC#CCC(NC(=O)C1CCCN1S(=O)(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 9, 21, 21, 23, 37, 37, 64, 64, 64, 64, 64, 23, 8, 1, 1, 1, 1, 1, 1, 1, 21, 21, 15, 21, 21] 145 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43]) total number of confs: 391 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918320 none CC#CCC(NC(=O)C1CCCN1S(=O)(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 93, 51, 51, 21, 51, 21, 21, 21, 21, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 93, 115, 115, 145, 145, 145, 145, 145, 93, 51, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 145 rigid atoms, others: [39, 40, 41, 42, 43, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 698 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918320 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918320 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918320/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918320 Building REAL300004918321 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918321' /scratch/stefan/7775246/working/building/REAL300004918321 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918321 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918321/0 /scratch/stefan/7775246/working/building/REAL300004918321 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/322 `/scratch/stefan/7775246/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C=C(NC(=O)C2=CC=CC(F)=C2)S1)C(=O)[O-]) `REAL300004918321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918321 none CC#CCC(NC(=O)C1=C(C)C=C(NC(=O)C2=CC=CC(F)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 1, 19, 30, 30, 47, 47, 47, 47, 47, 19, 8, 2, 2, 2, 1, 4, 11, 11, 11, 11] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918321 none CC#CCC(NC(=O)C1=C(C)C=C(NC(=O)C2=CC=CC(F)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 58, 58, 11, 58, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 110, 148, 148, 201, 201, 201, 201, 201, 110, 58, 11, 11, 11, 11, 5, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 976 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918321 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918321 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918321/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918321 Building REAL300004918322 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918322' /scratch/stefan/7775246/working/building/REAL300004918322 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918322 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918322/0 /scratch/stefan/7775246/working/building/REAL300004918322 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/323 `/scratch/stefan/7775246/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC2CCCC2)=C1)C(=O)[O-]) `REAL300004918322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918322 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 18, 18, 1, 17, 29, 29, 48, 48, 48, 48, 48, 17, 5, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 46, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918322 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 60, 60, 18, 60, 18, 18, 18, 18, 10, 4, 10, 10, 1, 1, 1, 1, 1, 1, 18, 132, 157, 157, 201, 201, 201, 201, 201, 132, 60, 18, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 951 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918322 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918322 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918322/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918322 Building REAL300004918323 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918323' /scratch/stefan/7775246/working/building/REAL300004918323 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918323 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918323/0 /scratch/stefan/7775246/working/building/REAL300004918323 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/324 `/scratch/stefan/7775246/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCC2CC2)=C1)C(=O)[O-]) `REAL300004918323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918323 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 21, 36, 36, 1, 13, 21, 21, 31, 31, 31, 31, 31, 13, 5, 1, 1, 1, 5, 21, 21, 36, 36, 36, 36, 36, 1] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918323 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 83, 83, 36, 83, 36, 36, 36, 36, 24, 18, 24, 24, 6, 1, 1, 1, 1, 36, 126, 161, 161, 201, 201, 201, 201, 201, 126, 83, 36, 36, 36, 18, 6, 6, 1, 1, 1, 1, 1, 36] 201 rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 987 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918323 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918323 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918323/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918323 Building REAL300004918324 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918324' /scratch/stefan/7775246/working/building/REAL300004918324 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918324 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918324/0 /scratch/stefan/7775246/working/building/REAL300004918324 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/325 `/scratch/stefan/7775246/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC(=O)C1=CC2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300004918324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918324 none CC#CCC(NC(=O)CCNC(=O)C1=CC2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 41, 41, 41, 21, 41, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 60, 60, 60, 60, 60, 41, 41, 21, 21, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918324 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918324 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918324/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918324 Building REAL300004918325 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918325' /scratch/stefan/7775246/working/building/REAL300004918325 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918325 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918325/0 /scratch/stefan/7775246/working/building/REAL300004918325 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/326 `/scratch/stefan/7775246/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(F)C=C1Br)C(=O)[O-]) `REAL300004918325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918325 none CC#CCC(NC(=O)C(C)OC1=CC=C(F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 59, 59, 13, 59, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 149, 149, 201, 201, 201, 201, 201, 102, 59, 13, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1029 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918325 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918325 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918325/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918325 Building REAL300004918326 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918326' /scratch/stefan/7775246/working/building/REAL300004918326 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918326 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918326/0 /scratch/stefan/7775246/working/building/REAL300004918326 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/327 `/scratch/stefan/7775246/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004918326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918326 none CC#CCC(NC(=O)C(C)SC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 76, 51, 51, 14, 51, 6, 14, 1, 1, 1, 1, 1, 1, 3, 1, 1, 76, 84, 84, 106, 106, 106, 106, 106, 76, 51, 14, 14, 14, 14, 1, 1, 3, 3, 3, 1, 1] 112 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918326 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918326 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918326/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918326 Building REAL300004918327 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918327' /scratch/stefan/7775246/working/building/REAL300004918327 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918327 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918327/0 /scratch/stefan/7775246/working/building/REAL300004918327 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/328 `/scratch/stefan/7775246/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918327 none CC#CCC(NC(=O)C(C)SC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 64, 64, 21, 64, 8, 21, 1, 1, 1, 1, 1, 1, 1, 1, 109, 146, 146, 201, 201, 201, 201, 201, 109, 64, 21, 21, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 991 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918327 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918327 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918327/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918327 Building REAL300004918328 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918328' /scratch/stefan/7775246/working/building/REAL300004918328 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918328 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918328/0 /scratch/stefan/7775246/working/building/REAL300004918328 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/329 `/scratch/stefan/7775246/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2)N1)C(=O)[O-]) `REAL300004918328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918328 none CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 71, 44, 44, 10, 44, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 72, 117, 117, 147, 147, 147, 147, 147, 72, 44, 10, 10, 7, 7, 1, 1, 7, 7, 1, 7, 7, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 839 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918328 none CC#CCC(NC(=O)CCC1=CC=C(C2=CC=CC=C2)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 113, 113, 34, 113, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 154, 186, 186, 201, 201, 201, 201, 201, 154, 113, 34, 34, 24, 24, 6, 7, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42]) total number of confs: 963 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918328 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918328 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918328/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918328 Building REAL300004918329 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918329' /scratch/stefan/7775246/working/building/REAL300004918329 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918329 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918329/0 /scratch/stefan/7775246/working/building/REAL300004918329 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/330 `/scratch/stefan/7775246/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC2=NC(C)=C(C)N=C21)C(=O)[O-]) `REAL300004918329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918329 none CC#CCC(NC(=O)C1=CC(F)=CC2=NC(C)=C(C)N=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 27, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 41, 41, 68, 68, 68, 68, 68, 27, 13, 1, 1, 2, 2, 2, 2, 2, 2] 68 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918329 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918329 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918329/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918329 Building REAL300004918330 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918330' /scratch/stefan/7775246/working/building/REAL300004918330 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918330 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918330/0 /scratch/stefan/7775246/working/building/REAL300004918330 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/331 `/scratch/stefan/7775246/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CS(=O)(=O)NC1=CC=C(OC(C)C)C=C1)C(=O)[O-]) `REAL300004918330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918330 none CC#CCC(NC(=O)CS(=O)(=O)NC1=CC=C(OC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 76, 59, 59, 20, 59, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 9, 18, 18, 1, 1, 76, 79, 79, 94, 94, 94, 94, 94, 76, 59, 20, 20, 4, 1, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [45, 36, 37, 46, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 444 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918330 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918330 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918330/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918330 Building REAL300004918331 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918331' /scratch/stefan/7775246/working/building/REAL300004918331 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918331 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918331/0 /scratch/stefan/7775246/working/building/REAL300004918331 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/332 `/scratch/stefan/7775246/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Cl)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004918331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918331 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Cl)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 4, 1, 1, 1, 40, 67, 67, 108, 108, 108, 108, 108, 40, 13, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 1] 139 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 555 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918331 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Cl)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 69, 25, 25, 4, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 69, 97, 97, 139, 139, 139, 139, 139, 69, 25, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 139 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 684 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918331 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918331 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918331/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918331 Building REAL300004918332 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918332' /scratch/stefan/7775246/working/building/REAL300004918332 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918332 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918332/0 /scratch/stefan/7775246/working/building/REAL300004918332 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/333 `/scratch/stefan/7775246/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(F)C(Br)=C1)C(=O)[O-]) `REAL300004918332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918332 none CC#CCC(NC(=O)CC1=CC=C(F)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 66, 18, 18, 8, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 113, 113, 201, 201, 201, 201, 201, 66, 18, 8, 8, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 1013 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918332 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918332 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918332/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918332 Building REAL300004918333 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918333' /scratch/stefan/7775246/working/building/REAL300004918333 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918333 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918333/0 /scratch/stefan/7775246/working/building/REAL300004918333 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/334 `/scratch/stefan/7775246/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CSCC)C=C1)C(=O)[O-]) `REAL300004918333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918333 none CC#CCC(NC(=O)C1=CC=C(CSCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 20, 33, 1, 1, 7, 11, 11, 21, 21, 21, 21, 21, 7, 3, 1, 1, 6, 6, 33, 33, 34, 34, 34, 1, 1] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 16, 17, 38, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918333 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918333 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918333/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918333 Building REAL300004918334 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918334' /scratch/stefan/7775246/working/building/REAL300004918334 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918334 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918334/0 /scratch/stefan/7775246/working/building/REAL300004918334 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/335 `/scratch/stefan/7775246/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC(OC)=C2OC1)C(=O)[O-]) `REAL300004918334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918334 none CC#CCC(NC(=O)C1=CC2=CC=CC(OC)=C2OC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 50, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 50, 80, 80, 137, 137, 137, 137, 137, 50, 13, 1, 1, 1, 1, 3, 3, 3, 1, 1] 172 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 16, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918334 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918334 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918334/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918334 Building REAL300004918335 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918335' /scratch/stefan/7775246/working/building/REAL300004918335 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918335 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918335/0 /scratch/stefan/7775246/working/building/REAL300004918335 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/336 `/scratch/stefan/7775246/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)NC(C)C)C=C1)C(=O)[O-]) `REAL300004918335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918335 none CC#CCC(NC(=O)C1=CC=C(NC(=O)NC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 14, 14, 14, 29, 29, 1, 1, 9, 15, 15, 34, 34, 34, 34, 34, 9, 3, 1, 1, 11, 14, 29, 29, 29, 29, 29, 29, 29, 1, 1] 201 rigid atoms, others: [32, 43, 6, 8, 9, 10, 11, 12, 19, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918335 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918335 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918335/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918335 Building REAL300004918336 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918336' /scratch/stefan/7775246/working/building/REAL300004918336 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918336 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918336/0 /scratch/stefan/7775246/working/building/REAL300004918336 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/337 `/scratch/stefan/7775246/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC(F)=C1)C(=O)[O-]) `REAL300004918336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918336 none CC#CCC(NC(=O)CCCOC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 85, 85, 35, 85, 27, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 118, 153, 153, 201, 201, 201, 201, 201, 118, 85, 35, 35, 27, 27, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1088 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918336 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918336 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918336/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918336 Building REAL300004918337 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918337' /scratch/stefan/7775246/working/building/REAL300004918337 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918337 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918337/0 /scratch/stefan/7775246/working/building/REAL300004918337 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/338 `/scratch/stefan/7775246/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1N=C(C2=CC=CC=C2)C=CC1=O)C(=O)[O-]) `REAL300004918337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918337 none CC#CCC(NC(=O)CN1N=C(C2=CC=CC=C2)C=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 63, 36, 36, 5, 36, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 63, 94, 94, 147, 147, 147, 147, 147, 63, 35, 5, 5, 6, 6, 1, 6, 6, 1, 1] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 40, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918337 none CC#CCC(NC(=O)CN1N=C(C2=CC=CC=C2)C=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 78, 78, 18, 78, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 124, 150, 150, 201, 201, 201, 201, 201, 124, 78, 18, 18, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40]) total number of confs: 940 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918337 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918337 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918337/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918337 Building REAL300004918338 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918338' /scratch/stefan/7775246/working/building/REAL300004918338 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918338 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918338/0 /scratch/stefan/7775246/working/building/REAL300004918338 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/339 `/scratch/stefan/7775246/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCCOC)C(=O)[O-]) `REAL300004918338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918338 none CC#CCC(NC(=O)C1=CC=CC=C1OCCOC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 9, 34, 51, 82, 16, 24, 24, 39, 39, 39, 39, 39, 16, 8, 1, 1, 1, 1, 34, 34, 51, 51, 82, 82, 82] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918338 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918338 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918338/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918338 Building REAL300004918339 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918339' /scratch/stefan/7775246/working/building/REAL300004918339 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918339 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918339/0 /scratch/stefan/7775246/working/building/REAL300004918339 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/340 `/scratch/stefan/7775246/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCCOC)=C1)C(=O)[O-]) `REAL300004918339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918339 none CC#CCC(NC(=O)C1=CC=CC(OCCOC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 12, 18, 34, 1, 13, 21, 21, 38, 38, 38, 38, 38, 13, 5, 1, 1, 1, 12, 12, 18, 18, 34, 34, 34, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 269 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918339 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918339 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918339/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918339 Building REAL300004918340 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918340' /scratch/stefan/7775246/working/building/REAL300004918340 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918340 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918340/0 /scratch/stefan/7775246/working/building/REAL300004918340 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/341 `/scratch/stefan/7775246/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(N2C(C)=CC=C2C)N(C)N=C1)C(=O)[O-]) `REAL300004918340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918340 none CC#CCC(NC(=O)C1=C(N2C(C)=CC=C2C)N(C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 1, 5, 8, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 44, 12, 12, 1, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 44, 58, 58, 87, 87, 87, 87, 87, 44, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 87 rigid atoms, others: [6, 8, 9, 10, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 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: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918340 none CC#CCC(NC(=O)C1=C(N2C(C)=CC=C2C)N(C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 1, 5, 8, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 46, 16, 16, 3, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 46, 60, 60, 87, 87, 87, 87, 87, 46, 16, 2, 2, 2, 1, 1, 2, 2, 2, 3, 3, 3, 3] 87 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918340 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918340 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918340/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918340 Building REAL300004918341 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918341' /scratch/stefan/7775246/working/building/REAL300004918341 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918341 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918341/0 /scratch/stefan/7775246/working/building/REAL300004918341 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/342 `/scratch/stefan/7775246/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)S2)=N1)C(=O)[O-]) `REAL300004918341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918341 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)S2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 33, 52, 52, 89, 89, 89, 89, 89, 33, 11, 1, 13, 13] 179 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918341 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)S2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 111, 57, 57, 13, 57, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 111, 139, 139, 179, 179, 179, 179, 179, 111, 57, 13, 1, 1] 179 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 842 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918341 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918341 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918341/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918341 Building REAL300004918342 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918342' /scratch/stefan/7775246/working/building/REAL300004918342 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918342 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918342/0 /scratch/stefan/7775246/working/building/REAL300004918342 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/343 `/scratch/stefan/7775246/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)CCC)C1)C(=O)[O-]) `REAL300004918342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918342 none CC#CCC(NC(=O)C1CCCN(C(=O)CCC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 32, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 10, 13, 1, 32, 48, 48, 77, 77, 77, 77, 77, 32, 13, 1, 1, 1, 1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 44, 43, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 417 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918342 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918342 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918342/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918342 Building REAL300004918343 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918343' /scratch/stefan/7775246/working/building/REAL300004918343 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918343 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918343/0 /scratch/stefan/7775246/working/building/REAL300004918343 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/344 `/scratch/stefan/7775246/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCN1C(=O)CCC)C(=O)[O-]) `REAL300004918343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918343 none CC#CCC(NC(=O)C1CCCCN1C(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 12, 9, 14, 14, 22, 22, 22, 22, 22, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13] 55 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918343 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918343 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918343/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918343 Building REAL300004918344 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918344' /scratch/stefan/7775246/working/building/REAL300004918344 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918344 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918344/0 /scratch/stefan/7775246/working/building/REAL300004918344 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/345 `/scratch/stefan/7775246/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=C([N+](=O)[O-])C=CC1=O)C(=O)[O-]) `REAL300004918344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918344 none CC#CCC(NC(=O)CN1C=C([N+](=O)[O-])C=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 11, 11, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 92, 37, 37, 5, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 135, 135, 201, 201, 201, 201, 201, 92, 37, 5, 5, 1, 1, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 971 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918344 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918344 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918344/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918344 Building REAL300004918345 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918345' /scratch/stefan/7775246/working/building/REAL300004918345 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918345 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918345/0 /scratch/stefan/7775246/working/building/REAL300004918345 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/346 `/scratch/stefan/7775246/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)N=N1)C(=O)[O-]) `REAL300004918345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918345 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 31, 41, 41, 55, 55, 55, 55, 55, 31, 10, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 276 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918345 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 40, 40, 5, 40, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 113, 152, 152, 201, 201, 201, 201, 201, 113, 40, 5, 5, 5, 1, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [34, 35, 36, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 1002 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918345 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918345 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918345/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918345 Building REAL300004918346 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918346' /scratch/stefan/7775246/working/building/REAL300004918346 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918346 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918346/0 /scratch/stefan/7775246/working/building/REAL300004918346 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/347 `/scratch/stefan/7775246/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300004918346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918346 none CC#CCC(NC(=O)CCC1=CC2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 57, 28, 28, 6, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 73, 73, 83, 83, 83, 83, 83, 57, 28, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/7775246/working/building/REAL300004918346 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918346 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918346/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918346 Building REAL300004918347 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918347' /scratch/stefan/7775246/working/building/REAL300004918347 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918347 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918347/0 /scratch/stefan/7775246/working/building/REAL300004918347 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/348 `/scratch/stefan/7775246/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-]) `REAL300004918347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918347 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 24, 5, 5, 1, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 24, 40, 40, 79, 79, 79, 79, 79, 24, 5, 1, 7, 7, 6, 7, 1] 167 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918347 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 82, 25, 25, 7, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 82, 109, 109, 167, 167, 167, 167, 167, 82, 25, 7, 1, 1, 1, 1, 7] 167 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918347 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918347 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918347/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918347 Building REAL300004918348 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918348' /scratch/stefan/7775246/working/building/REAL300004918348 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918348 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918348/0 /scratch/stefan/7775246/working/building/REAL300004918348 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/349 `/scratch/stefan/7775246/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2)C=C1)C(=O)[O-]) `REAL300004918348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918348 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 37, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 6, 6, 7, 6, 1, 1, 37, 56, 56, 91, 91, 91, 91, 91, 37, 11, 6, 7, 6, 7, 1, 1] 147 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918348 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 84, 40, 40, 6, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 84, 109, 109, 147, 147, 147, 147, 147, 84, 40, 1, 1, 1, 1, 6, 6] 147 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918348 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918348 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918348/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918348 Building REAL300004918349 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918349' /scratch/stefan/7775246/working/building/REAL300004918349 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918349 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918349/0 /scratch/stefan/7775246/working/building/REAL300004918349 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/350 `/scratch/stefan/7775246/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2OC)=N1)C(=O)[O-]) `REAL300004918349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918349 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2OC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 25, 1, 19, 31, 31, 57, 57, 57, 57, 57, 19, 9, 1, 12, 12, 12, 12, 26, 26, 26] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918349 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2OC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 98, 43, 43, 12, 43, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 98, 138, 138, 190, 190, 190, 190, 190, 98, 43, 12, 1, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918349 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918349 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918349/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918349 Building REAL300004918350 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918350' /scratch/stefan/7775246/working/building/REAL300004918350 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918350 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918350/0 /scratch/stefan/7775246/working/building/REAL300004918350 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/351 `/scratch/stefan/7775246/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CN2N=C(C)C=C2C)=C1)C(=O)[O-]) `REAL300004918350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918350 none CC#CCC(NC(=O)C1=CC=CC(CN2N=C(C)C=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 1, 17, 23, 23, 49, 49, 49, 49, 49, 17, 5, 1, 1, 1, 6, 6, 16, 16, 16, 15, 16, 16, 16, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 44, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918350 none CC#CCC(NC(=O)C1=CC=CC(CN2N=C(C)C=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 95, 42, 42, 15, 42, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 95, 126, 126, 201, 201, 201, 201, 201, 95, 42, 15, 15, 15, 4, 4, 2, 2, 2, 1, 2, 2, 2, 15] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 945 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918350 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918350 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918350/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918350 Building REAL300004918351 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918351' /scratch/stefan/7775246/working/building/REAL300004918351 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918351 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918351/0 /scratch/stefan/7775246/working/building/REAL300004918351 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/352 `/scratch/stefan/7775246/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CS(=O)(=O)NC(C)(C)C)=C1)C(=O)[O-]) `REAL300004918351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918351 none CC#CCC(NC(=O)C1=CC=CC(CS(=O)(=O)NC(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 30, 30, 30, 30, 1, 14, 21, 21, 41, 41, 41, 41, 41, 14, 5, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 48, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 293 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918351 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918351 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918351/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918351 Building REAL300004918352 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918352' /scratch/stefan/7775246/working/building/REAL300004918352 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918352 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918352/0 /scratch/stefan/7775246/working/building/REAL300004918352 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/353 `/scratch/stefan/7775246/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COC2=CC(OC)=CC=C2C1)C(=O)[O-]) `REAL300004918352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918352 none CC#CCC(NC(=O)C1COC2=CC(OC)=CC=C2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 52, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 52, 76, 76, 124, 124, 124, 124, 124, 52, 13, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 40, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 15, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 584 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918352 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918352 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918352/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918352 Building REAL300004918353 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918353' /scratch/stefan/7775246/working/building/REAL300004918353 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918353 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918353/0 /scratch/stefan/7775246/working/building/REAL300004918353 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/354 `/scratch/stefan/7775246/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=C2OCCOC2=C1)C(=O)[O-]) `REAL300004918353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918353 none CC#CCC(NC(=O)C1=CC(Br)=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 37, 37, 68, 68, 68, 68, 68, 26, 7, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918353 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918353 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918353/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918353 Building REAL300004918354 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918354' /scratch/stefan/7775246/working/building/REAL300004918354 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918354 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918354/0 /scratch/stefan/7775246/working/building/REAL300004918354 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/355 `/scratch/stefan/7775246/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918354 none CC#CCC(NC(=O)C1=CC=C(OC)C(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 1, 1, 6, 6, 3, 6, 6, 1, 26, 44, 44, 99, 99, 99, 99, 99, 26, 7, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 14, 15, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918354 none CC#CCC(NC(=O)C1=CC=C(OC)C(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 64, 22, 22, 6, 22, 6, 6, 6, 6, 6, 11, 1, 1, 1, 1, 1, 1, 1, 6, 64, 103, 103, 175, 175, 175, 175, 175, 64, 22, 6, 6, 11, 11, 11, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 848 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918354 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918354 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918354/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918354 Building REAL300004918355 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918355' /scratch/stefan/7775246/working/building/REAL300004918355 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918355 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918355/0 /scratch/stefan/7775246/working/building/REAL300004918355 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/356 `/scratch/stefan/7775246/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC=C2OC)CC1)C(=O)[O-]) `REAL300004918355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918355 none CC#CCC(NC(=O)C1(C2=CC=CC=C2OC)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 44, 13, 13, 1, 13, 1, 1, 5, 5, 2, 5, 5, 5, 9, 1, 1, 44, 70, 70, 130, 130, 130, 130, 130, 44, 13, 5, 5, 4, 5, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 626 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918355 none CC#CCC(NC(=O)C1(C2=CC=CC=C2OC)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 78, 29, 29, 5, 29, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 78, 119, 119, 190, 190, 190, 190, 190, 78, 29, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 922 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918355 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918355 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918355/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918355 Building REAL300004918356 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918356' /scratch/stefan/7775246/working/building/REAL300004918356 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918356 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918356/0 /scratch/stefan/7775246/working/building/REAL300004918356 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/357 `/scratch/stefan/7775246/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC=CC=C2)C1)C(=O)[O-]) `REAL300004918356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918356 none CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 39, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 6, 13, 13, 1, 39, 61, 61, 103, 103, 103, 103, 103, 39, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 9, 13, 13, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 44, 21, 45, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43]) total number of confs: 540 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918356 none CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 74, 74, 13, 74, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 135, 166, 166, 201, 201, 201, 201, 201, 135, 74, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13] 201 rigid atoms, others: [39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 928 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918356 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918356 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918356/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918356 Building REAL300004918357 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918357' /scratch/stefan/7775246/working/building/REAL300004918357 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918357 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918357/0 /scratch/stefan/7775246/working/building/REAL300004918357 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/358 `/scratch/stefan/7775246/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918357 none CC#CCC(NC(=O)C(C)OC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 84, 84, 20, 84, 8, 20, 1, 1, 1, 1, 1, 1, 1, 1, 128, 160, 160, 201, 201, 201, 201, 201, 128, 84, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1002 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918357 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918357 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918357/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918357 Building REAL300004918358 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918358' /scratch/stefan/7775246/working/building/REAL300004918358 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918358 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918358/0 /scratch/stefan/7775246/working/building/REAL300004918358 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/359 `/scratch/stefan/7775246/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1S(=O)(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004918358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918358 none CC#CCC(NC(=O)C1CCCN1S(=O)(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 18, 27, 27, 38, 38, 38, 38, 38, 18, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20] 88 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 225 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918358 none CC#CCC(NC(=O)C1CCCN1S(=O)(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 54, 32, 32, 20, 32, 20, 20, 20, 20, 9, 1, 9, 9, 1, 1, 1, 1, 1, 54, 67, 67, 88, 88, 88, 88, 88, 54, 32, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1] 88 rigid atoms, others: [38, 39, 40, 13, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 416 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918358 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918358 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918358/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918358 Building REAL300004918359 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918359' /scratch/stefan/7775246/working/building/REAL300004918359 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918359 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918359/0 /scratch/stefan/7775246/working/building/REAL300004918359 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/360 `/scratch/stefan/7775246/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1)C(=O)[O-]) `REAL300004918359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918359 none CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 1, 17, 33, 33, 81, 81, 81, 81, 81, 17, 5, 1, 1, 1, 5, 5, 9, 9, 9, 9, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 381 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918359 none CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 87, 27, 27, 9, 27, 9, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 87, 130, 130, 201, 201, 201, 201, 201, 87, 27, 9, 9, 9, 4, 4, 1, 1, 1, 1, 9] 201 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 1010 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918359 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918359 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918359/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918359 Building REAL300004918360 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918360' /scratch/stefan/7775246/working/building/REAL300004918360 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918360 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918360/0 /scratch/stefan/7775246/working/building/REAL300004918360 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/361 `/scratch/stefan/7775246/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCCCC1)C(=O)[O-]) `REAL300004918360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918360 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 18, 5, 5, 1, 5, 1, 1, 13, 13, 1, 13, 13, 13, 1, 1, 1, 1, 1, 18, 32, 32, 54, 54, 54, 54, 54, 18, 5, 13, 13, 9, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 42, 43, 44, 16, 17, 18, 19, 20, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918360 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 36, 36, 13, 36, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 98, 133, 133, 201, 201, 201, 201, 201, 98, 36, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 987 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918360 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918360 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918360/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918360 Building REAL300004918361 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918361' /scratch/stefan/7775246/working/building/REAL300004918361 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918361 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918361/0 /scratch/stefan/7775246/working/building/REAL300004918361 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/362 `/scratch/stefan/7775246/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC(C)=CC(C)=C2)C(C)=C1)C(=O)[O-]) `REAL300004918361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918361 none CC#CCC(NC(=O)C1=C(C)N(C2=CC(C)=CC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 48, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 4, 2, 4, 4, 4, 1, 1, 1, 48, 66, 66, 98, 98, 98, 98, 98, 48, 13, 2, 2, 2, 4, 4, 4, 4, 3, 4, 4, 4, 4, 2, 2, 2, 1] 167 rigid atoms, others: [6, 8, 9, 10, 11, 12, 48, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 481 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918361 none CC#CCC(NC(=O)C1=C(C)N(C2=CC(C)=CC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 100, 36, 36, 4, 36, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 100, 121, 121, 167, 167, 167, 167, 167, 100, 36, 4, 4, 4, 1, 2, 2, 2, 1, 2, 2, 2, 1, 4, 4, 4, 4] 167 rigid atoms, others: [36, 40, 44, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 759 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918361 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918361 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918361/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918361 Building REAL300004918362 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918362' /scratch/stefan/7775246/working/building/REAL300004918362 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918362 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918362/0 /scratch/stefan/7775246/working/building/REAL300004918362 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/363 `/scratch/stefan/7775246/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C1=C2C=CSC2=NC=N1)C(=O)[O-]) `REAL300004918362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918362 none CC#CCC(NC(=O)C1CCCN1C1=C2C=CSC2=NC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 1, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 4, 5, 5, 36, 53, 53, 80, 80, 80, 80, 80, 36, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 124 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 387 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918362 none CC#CCC(NC(=O)C1CCCN1C1=C2C=CSC2=NC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 1, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 72, 28, 28, 5, 28, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 94, 94, 124, 124, 124, 124, 124, 72, 28, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 124 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 592 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918362 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918362 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918362/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918362 Building REAL300004918363 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918363' /scratch/stefan/7775246/working/building/REAL300004918363 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918363 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918363/0 /scratch/stefan/7775246/working/building/REAL300004918363 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/364 `/scratch/stefan/7775246/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)OC(C2=CC=CO2)=N1)C(=O)[O-]) `REAL300004918363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918363 none CC#CCC(NC(=O)CC1=C(C)OC(C2=CC=CO2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 68, 36, 36, 8, 36, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 68, 101, 101, 147, 147, 147, 147, 147, 68, 36, 8, 8, 1, 1, 1, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918363 none CC#CCC(NC(=O)CC1=C(C)OC(C2=CC=CO2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 59, 59, 17, 59, 7, 6, 6, 7, 6, 1, 1, 1, 1, 1, 1, 6, 102, 148, 148, 201, 201, 201, 201, 201, 102, 59, 17, 17, 7, 7, 7, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1034 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918363 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918363 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918363/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918363 Building REAL300004918364 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918364' /scratch/stefan/7775246/working/building/REAL300004918364 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918364 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918364/0 /scratch/stefan/7775246/working/building/REAL300004918364 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/365 `/scratch/stefan/7775246/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2N=C(C)C([N+](=O)[O-])=C2C)C=C1)C(=O)[O-]) `REAL300004918364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918364 none CC#CCC(NC(=O)C1=CC=C(CN2N=C(C)C([N+](=O)[O-])=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 8, 11, 11, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 21, 22, 22, 21, 22, 1, 1, 9, 16, 16, 26, 26, 26, 26, 26, 9, 3, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918364 none CC#CCC(NC(=O)C1=CC=C(CN2N=C(C)C([N+](=O)[O-])=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 8, 11, 11, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 40, 40, 22, 40, 11, 22, 21, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 22, 109, 140, 140, 201, 201, 201, 201, 201, 109, 40, 22, 22, 5, 5, 2, 2, 2, 2, 2, 2, 22, 22] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1046 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918364 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918364 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918364/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918364 Building REAL300004918365 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918365' /scratch/stefan/7775246/working/building/REAL300004918365 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004918365 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918365/0 /scratch/stefan/7775246/working/building/REAL300004918365 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/366 `/scratch/stefan/7775246/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C(=S)NN=C1C1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918365 none CC#CCC(NC(=O)CN1C(=S)NN=C1C1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'S.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 14, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 79, 26, 26, 4, 26, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 79, 122, 122, 187, 187, 187, 187, 187, 79, 26, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 949 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918365 none CC#CCC(NC(=O)CN1C(=S)NN=C1C1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'S.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 14, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 56, 56, 9, 56, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 118, 153, 153, 201, 201, 201, 201, 201, 118, 56, 9, 9, 5, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [35, 36, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 960 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918365 /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `1' /scratch/stefan/7775246/working/building/REAL300004918365/1 /scratch/stefan/7775246/working/building/REAL300004918365 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/367 `/scratch/stefan/7775246/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C(=S)[N-]N=C1C1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918365.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004918365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918365 none CC#CCC(NC(=O)CN1C(=S)[N-]N=C1C1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'S.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 14, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 75, 26, 26, 4, 26, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 75, 105, 105, 179, 179, 179, 179, 179, 75, 26, 4, 4, 6, 6, 6, 6, 6, 6, 6] 189 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 882 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918365 none CC#CCC(NC(=O)CN1C(=S)[N-]N=C1C1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'S.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 14, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 115, 57, 57, 10, 57, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 115, 144, 144, 189, 189, 189, 189, 189, 115, 57, 10, 10, 1, 1, 2, 2, 2, 1, 1] 189 rigid atoms, others: [34, 35, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 908 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918365 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918365 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918365/0.* 1: /scratch/stefan/7775246/working/building/REAL300004918365/1.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918365 Building REAL300004918366 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918366' /scratch/stefan/7775246/working/building/REAL300004918366 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918366 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918366/0 /scratch/stefan/7775246/working/building/REAL300004918366 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/368 `/scratch/stefan/7775246/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=C(C)C=C2)=N1)C(=O)[O-]) `REAL300004918366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918366 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 44, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 44, 57, 57, 61, 61, 61, 61, 61, 44, 20, 7, 7, 1, 3, 3, 4, 4, 4, 3, 3] 67 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918366 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 57, 33, 33, 14, 33, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 57, 63, 63, 67, 67, 67, 67, 67, 57, 33, 14, 14, 3, 1, 1, 2, 2, 2, 1, 1] 67 rigid atoms, others: [34, 35, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918366 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918366 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918366/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918366 Building REAL300004918367 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918367' /scratch/stefan/7775246/working/building/REAL300004918367 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918367 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918367/0 /scratch/stefan/7775246/working/building/REAL300004918367 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/369 `/scratch/stefan/7775246/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OC(F)F)C=C1)C(=O)[O-]) `REAL300004918367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918367 none CC#CCC(NC(=O)CC1=CC=C(OC(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 24, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 12, 22, 22, 1, 1, 24, 37, 37, 49, 49, 49, 49, 49, 24, 9, 3, 3, 1, 1, 22, 1, 1] 201 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918367 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918367 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918367/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918367 Building REAL300004918368 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918368' /scratch/stefan/7775246/working/building/REAL300004918368 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918368 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918368/0 /scratch/stefan/7775246/working/building/REAL300004918368 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/370 `/scratch/stefan/7775246/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)CC(C)N2S(C)(=O)=O)C(=O)[O-]) `REAL300004918368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918368 none CC#CCC(NC(=O)C1=CC=C2C(=C1)CC(C)N2S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 40, 40, 80, 80, 80, 80, 80, 27, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6] 159 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918368 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918368 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918368/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918368 Building REAL300004918369 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918369' /scratch/stefan/7775246/working/building/REAL300004918369 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918369 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918369/0 /scratch/stefan/7775246/working/building/REAL300004918369 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/371 `/scratch/stefan/7775246/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=C(SC=C2)S1)C(=O)[O-]) `REAL300004918369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918369 none CC#CCC(NC(=O)C1=C(Cl)C2=C(SC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 62, 62, 62, 62, 62, 25, 6, 1, 1] 62 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918369 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918369 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918369/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918369 Building REAL300004918370 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918370' /scratch/stefan/7775246/working/building/REAL300004918370 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918370 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918370/0 /scratch/stefan/7775246/working/building/REAL300004918370 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/372 `/scratch/stefan/7775246/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(F)C=CC=C2S1)C(=O)[O-]) `REAL300004918370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918370 none CC#CCC(NC(=O)C1=C(C)C2=C(F)C=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 15, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 46, 46, 64, 64, 64, 64, 64, 31, 10, 2, 2, 2, 1, 1, 1] 64 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918370 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918370 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918370/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918370 Building REAL300004918371 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918371' /scratch/stefan/7775246/working/building/REAL300004918371 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918371 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918371/0 /scratch/stefan/7775246/working/building/REAL300004918371 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/373 `/scratch/stefan/7775246/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(Br)=C1)C(=O)[O-]) `REAL300004918371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918371 none CC#CCC(NC(=O)C1=CC=C(OC)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 1, 1, 1, 30, 48, 48, 89, 89, 89, 89, 89, 30, 7, 1, 1, 4, 4, 4, 1] 148 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918371 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918371 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918371/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918371 Building REAL300004918372 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918372' /scratch/stefan/7775246/working/building/REAL300004918372 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918372 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918372/0 /scratch/stefan/7775246/working/building/REAL300004918372 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/374 `/scratch/stefan/7775246/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(C)OC)=C1)C(=O)[O-]) `REAL300004918372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918372 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(C)OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 24, 1, 14, 22, 22, 36, 36, 36, 36, 36, 14, 5, 1, 1, 1, 15, 15, 15, 24, 24, 24, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918372 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918372 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918372/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918372 Building REAL300004918373 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918373' /scratch/stefan/7775246/working/building/REAL300004918373 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918373 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918373/0 /scratch/stefan/7775246/working/building/REAL300004918373 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/375 `/scratch/stefan/7775246/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C2OCCCOC2=C1)C(=O)[O-]) `REAL300004918373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918373 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C2OCCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 46, 46, 6, 46, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 153, 153, 201, 201, 201, 201, 201, 123, 46, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 899 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918373 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918373 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918373/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918373 Building REAL300004918374 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918374' /scratch/stefan/7775246/working/building/REAL300004918374 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918374 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918374/0 /scratch/stefan/7775246/working/building/REAL300004918374 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/376 `/scratch/stefan/7775246/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN(C)C1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918374 none CC#CCC(NC(=O)CN(C)C1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 5, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 36, 20, 20, 9, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 38, 38, 46, 46, 46, 46, 46, 36, 20, 9, 9, 7, 7, 7, 1, 1, 1, 1] 46 rigid atoms, others: [37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918374 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918374 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918374/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918374 Building REAL300004918375 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918375' /scratch/stefan/7775246/working/building/REAL300004918375 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918375 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918375/0 /scratch/stefan/7775246/working/building/REAL300004918375 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/377 `/scratch/stefan/7775246/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(Cl)C2=CC=CC=C2S1)C(=O)[O-]) `REAL300004918375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918375 none CC#CCC(NC(=O)C=CC1=C(Cl)C2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 68, 68, 10, 67, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 155, 155, 201, 201, 201, 201, 201, 126, 68, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 904 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918375 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918375 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918375/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918375 Building REAL300004918376 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918376' /scratch/stefan/7775246/working/building/REAL300004918376 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918376 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918376/0 /scratch/stefan/7775246/working/building/REAL300004918376 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/378 `/scratch/stefan/7775246/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(COC)C2=C(F)C=CC=C2S1)C(=O)[O-]) `REAL300004918376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918376 none CC#CCC(NC(=O)C1=C(COC)C2=C(F)C=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 1, 1, 15, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 36, 12, 12, 1, 12, 1, 1, 1, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 36, 63, 63, 112, 112, 112, 112, 112, 36, 12, 6, 6, 22, 22, 22, 1, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918376 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918376 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918376/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918376 Building REAL300004918377 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918377' /scratch/stefan/7775246/working/building/REAL300004918377 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918377 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918377/0 /scratch/stefan/7775246/working/building/REAL300004918377 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/379 `/scratch/stefan/7775246/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C2OCCCOC2=C1)C(=O)[O-]) `REAL300004918377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918377 none CC#CCC(NC(=O)C1=CC(Cl)=C2OCCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 39, 39, 71, 71, 71, 71, 71, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918377 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918377 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918377/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918377 Building REAL300004918378 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918378' /scratch/stefan/7775246/working/building/REAL300004918378 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918378 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918378/0 /scratch/stefan/7775246/working/building/REAL300004918378 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/380 `/scratch/stefan/7775246/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=NOC(C)=C2)C(C)=C1)C(=O)[O-]) `REAL300004918378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918378 none CC#CCC(NC(=O)C1=C(C)N(C2=NOC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 8, 12, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 35, 13, 13, 1, 13, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 1, 35, 56, 56, 90, 90, 90, 90, 90, 35, 13, 2, 2, 2, 11, 11, 11, 11, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 467 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918378 none CC#CCC(NC(=O)C1=C(C)N(C2=NOC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 8, 12, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 70, 70, 11, 70, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 127, 155, 155, 201, 201, 201, 201, 201, 127, 70, 11, 11, 11, 2, 2, 2, 1, 11, 11, 11, 11] 201 rigid atoms, others: [37, 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, 38, 39, 40, 41]) total number of confs: 896 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918378 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918378 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918378/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918378 Building REAL300004918379 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918379' /scratch/stefan/7775246/working/building/REAL300004918379 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918379 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918379/0 /scratch/stefan/7775246/working/building/REAL300004918379 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/381 `/scratch/stefan/7775246/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N(C)OC)=C1)C(=O)[O-]) `REAL300004918379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918379 none CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N(C)OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 15, 1, 17, 26, 26, 52, 52, 52, 52, 52, 17, 5, 1, 1, 11, 11, 11, 15, 15, 15, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918379 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918379 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918379/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918379 Building REAL300004918380 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918380' /scratch/stefan/7775246/working/building/REAL300004918380 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918380 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918380/0 /scratch/stefan/7775246/working/building/REAL300004918380 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/382 `/scratch/stefan/7775246/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=CC=C2Cl)=N1)C(=O)[O-]) `REAL300004918380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918380 none CC#CCC(NC(=O)CC1=CSC(C2=CC=CC=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 28, 28, 6, 28, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 1, 49, 81, 81, 103, 103, 103, 103, 103, 49, 28, 6, 6, 1, 8, 8, 3, 8] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918380 none CC#CCC(NC(=O)CC1=CSC(C2=CC=CC=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 89, 89, 27, 89, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 130, 156, 156, 201, 201, 201, 201, 201, 130, 89, 27, 27, 8, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 959 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918380 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918380 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918380/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918380 Building REAL300004918381 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918381' /scratch/stefan/7775246/working/building/REAL300004918381 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918381 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918381/0 /scratch/stefan/7775246/working/building/REAL300004918381 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/383 `/scratch/stefan/7775246/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004918381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918381 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 37, 54, 54, 75, 75, 75, 75, 75, 37, 12, 2, 2, 2, 4, 4, 2, 4, 4] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 380 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918381 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 54, 29, 29, 4, 29, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 54, 63, 63, 79, 79, 79, 79, 79, 54, 29, 4, 4, 4, 1, 1, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 349 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918381 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918381 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918381/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918381 Building REAL300004918382 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918382' /scratch/stefan/7775246/working/building/REAL300004918382 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918382 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918382/0 /scratch/stefan/7775246/working/building/REAL300004918382 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/384 `/scratch/stefan/7775246/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CS2)S1)C(=O)[O-]) `REAL300004918382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918382 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CS2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 14, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 1, 32, 52, 52, 93, 93, 93, 93, 93, 32, 10, 2, 2, 2, 13, 13, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 461 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918382 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CS2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 14, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 75, 75, 12, 74, 12, 12, 13, 12, 1, 1, 1, 1, 1, 1, 13, 133, 169, 169, 201, 201, 201, 201, 201, 133, 75, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 931 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918382 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918382 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918382/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918382 Building REAL300004918383 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918383' /scratch/stefan/7775246/working/building/REAL300004918383 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918383 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918383/0 /scratch/stefan/7775246/working/building/REAL300004918383 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/385 `/scratch/stefan/7775246/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-]) `REAL300004918383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918383 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 1, 43, 63, 63, 102, 102, 102, 102, 102, 43, 12, 2, 2, 2, 4, 4, 2, 4] 151 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 494 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918383 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 91, 38, 38, 4, 38, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 91, 112, 112, 151, 151, 151, 151, 151, 91, 38, 5, 5, 5, 1, 1, 1, 1] 151 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 684 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918383 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918383 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918383/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918383 Building REAL300004918384 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918384' /scratch/stefan/7775246/working/building/REAL300004918384 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918384 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918384/0 /scratch/stefan/7775246/working/building/REAL300004918384 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/386 `/scratch/stefan/7775246/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC(Cl)=C2)=N1)C(=O)[O-]) `REAL300004918384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918384 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC(Cl)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 36, 54, 54, 93, 93, 93, 93, 93, 36, 11, 1, 5, 5, 3, 5] 142 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918384 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC(Cl)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 79, 35, 35, 5, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 79, 106, 106, 142, 142, 142, 142, 142, 79, 35, 5, 1, 1, 1, 1] 142 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918384 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918384 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918384/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918384 Building REAL300004918385 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918385' /scratch/stefan/7775246/working/building/REAL300004918385 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918385 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918385/0 /scratch/stefan/7775246/working/building/REAL300004918385 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/387 `/scratch/stefan/7775246/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918385 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 37, 55, 55, 84, 84, 84, 84, 84, 37, 13, 1, 4, 4, 2, 4, 4] 88 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918385 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 59, 29, 29, 4, 29, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 59, 72, 72, 88, 88, 88, 88, 88, 59, 29, 4, 1, 1, 1, 1, 1] 88 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918385 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918385 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918385/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918385 Building REAL300004918386 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918386' /scratch/stefan/7775246/working/building/REAL300004918386 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918386 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918386/0 /scratch/stefan/7775246/working/building/REAL300004918386 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/388 `/scratch/stefan/7775246/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC(OC)=C1OC(F)F)C(=O)[O-]) `REAL300004918386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918386 none CC#CCC(NC(=O)C=CC1=CC=CC(OC)=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 43, 25, 25, 9, 25, 9, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 6, 24, 24, 43, 59, 59, 95, 95, 95, 95, 95, 43, 25, 9, 9, 1, 1, 1, 4, 4, 4, 24] 201 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 535 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918386 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918386 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918386/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918386 Building REAL300004918387 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918387' /scratch/stefan/7775246/working/building/REAL300004918387 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918387 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918387/0 /scratch/stefan/7775246/working/building/REAL300004918387 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/389 `/scratch/stefan/7775246/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(F)C(F)=C1)C(=O)[O-]) `REAL300004918387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918387 none CC#CCC(NC(=O)CSC1=CC=C(F)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 15, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 80, 80, 23, 80, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 150, 150, 201, 201, 201, 201, 201, 120, 79, 23, 23, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 964 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918387 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918387 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918387/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918387 Building REAL300004918388 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918388' /scratch/stefan/7775246/working/building/REAL300004918388 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918388 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918388/0 /scratch/stefan/7775246/working/building/REAL300004918388 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/390 `/scratch/stefan/7775246/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC(=O)N(C)C)C(=O)[O-]) `REAL300004918388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918388 none CC#CCC(NC(=O)C1=CC=CC=C1OCC(=O)N(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 9, 32, 69, 69, 75, 75, 20, 30, 30, 53, 53, 53, 53, 53, 20, 9, 1, 1, 1, 1, 32, 32, 75, 75, 75, 75, 75, 75] 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, 40, 41, 42]) total number of confs: 496 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918388 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918388 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918388/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918388 Building REAL300004918389 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918389' /scratch/stefan/7775246/working/building/REAL300004918389 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918389 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918389/0 /scratch/stefan/7775246/working/building/REAL300004918389 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/391 `/scratch/stefan/7775246/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2CCCCC2)C(C)=C1)C(=O)[O-]) `REAL300004918389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918389 none CC#CCC(NC(=O)C1=C(C)N(C2CCCCC2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 42, 12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 42, 63, 63, 96, 96, 96, 96, 96, 42, 12, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1] 139 rigid atoms, others: [6, 8, 9, 10, 11, 12, 48, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 478 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918389 none CC#CCC(NC(=O)C1=C(C)N(C2CCCCC2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 68, 24, 24, 3, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 68, 90, 90, 139, 139, 139, 139, 139, 68, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 139 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 43, 44] 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, 45, 46, 47, 48]) total number of confs: 639 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918389 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918389 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918389/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918389 Building REAL300004918390 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918390' /scratch/stefan/7775246/working/building/REAL300004918390 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918390 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918390/0 /scratch/stefan/7775246/working/building/REAL300004918390 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/392 `/scratch/stefan/7775246/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=CS2)=N1)C(=O)[O-]) `REAL300004918390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918390 none CC#CCC(NC(=O)CC1=CSC(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 71, 39, 39, 8, 39, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 71, 111, 111, 156, 156, 156, 156, 156, 71, 39, 8, 8, 1, 8, 8, 8] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918390 none CC#CCC(NC(=O)CC1=CSC(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 114, 74, 74, 24, 74, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 114, 155, 155, 201, 201, 201, 201, 201, 114, 74, 24, 24, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1018 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918390 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918390 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918390/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918390 Building REAL300004918391 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918391' /scratch/stefan/7775246/working/building/REAL300004918391 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918391 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918391/0 /scratch/stefan/7775246/working/building/REAL300004918391 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/393 `/scratch/stefan/7775246/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=C(C)C=C2)C=CS1)C(=O)[O-]) `REAL300004918391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918391 none CC#CCC(NC(=O)C1=C(C2=CC=C(C)C=C2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 49, 12, 13, 1, 13, 1, 1, 1, 6, 6, 2, 5, 6, 6, 1, 1, 1, 49, 81, 81, 133, 133, 133, 133, 133, 49, 13, 6, 6, 6, 6, 6, 6, 6, 1, 1] 160 rigid atoms, others: [37, 6, 8, 9, 10, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918391 none CC#CCC(NC(=O)C1=C(C2=CC=C(C)C=C2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 86, 33, 33, 6, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 86, 119, 119, 160, 160, 160, 160, 160, 86, 33, 1, 1, 2, 2, 2, 1, 1, 6, 6] 160 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) total number of confs: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918391 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918391 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918391/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918391 Building REAL300004918392 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918392' /scratch/stefan/7775246/working/building/REAL300004918392 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918392 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918392/0 /scratch/stefan/7775246/working/building/REAL300004918392 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/394 `/scratch/stefan/7775246/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNS(=O)(=O)C1=CC=CC(C(=O)NC(CC#CC)C(=O)[O-])=C1) `REAL300004918392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918392 none C#CCNS(=O)(=O)C1=CC=CC(C(=O)NC(CC#CC)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', '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.3', 'C.1', 'C.1', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 6, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 39, 39, 39, 15, 23, 23, 1, 25, 25, 25, 6, 1, 1, 1, 5, 15, 39, 39, 39, 39, 39, 1] 201 rigid atoms, others: [4, 38, 7, 8, 9, 10, 11, 12, 23, 28, 29, 30] set([0, 1, 2, 3, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918392 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918392 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918392/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918392 Building REAL300004918393 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918393' /scratch/stefan/7775246/working/building/REAL300004918393 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918393 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918393/0 /scratch/stefan/7775246/working/building/REAL300004918393 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/395 `/scratch/stefan/7775246/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNS(=O)(=O)C1=CC=C(C(=O)NC(CC#CC)C(=O)[O-])C=C1) `REAL300004918393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300004918393 0 /scratch/stefan/7775246/working/building/REAL300004918393 /scratch/stefan/7775246/working /scratch/stefan/7775246 `0' -> `0.failed' Finished preparing REAL300004918393 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Found failed protomers Marking REAL300004918393 as failed mkdir: created directory `/scratch/stefan/7775246/failed' `/scratch/stefan/7775246/working/building/REAL300004918393' -> `/scratch/stefan/7775246/failed/REAL300004918393' Building REAL300004918394 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918394' /scratch/stefan/7775246/working/building/REAL300004918394 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918394 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918394/0 /scratch/stefan/7775246/working/building/REAL300004918394 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/396 `/scratch/stefan/7775246/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCCOC)C=C1)C(=O)[O-]) `REAL300004918394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918394 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCCOC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 31, 41, 1, 1, 9, 13, 13, 24, 24, 24, 24, 24, 9, 3, 1, 1, 9, 25, 25, 31, 31, 41, 41, 41, 1, 1] 201 rigid atoms, others: [32, 33, 43, 6, 8, 9, 10, 11, 12, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918394 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918394 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918394/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918394 Building REAL300004918395 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918395' /scratch/stefan/7775246/working/building/REAL300004918395 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918395 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918395/0 /scratch/stefan/7775246/working/building/REAL300004918395 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/397 `/scratch/stefan/7775246/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC2CC2)=CC=C1C)C(=O)[O-]) `REAL300004918395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918395 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC2CC2)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 19, 9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 1, 1, 19, 31, 31, 53, 53, 53, 53, 53, 19, 9, 1, 9, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 40, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918395 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC2CC2)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 86, 86, 25, 86, 25, 25, 14, 5, 14, 14, 1, 1, 1, 1, 25, 25, 25, 25, 126, 166, 166, 201, 201, 201, 201, 201, 126, 86, 25, 5, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43]) total number of confs: 993 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918395 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918395 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918395/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918395 Building REAL300004918396 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918396' /scratch/stefan/7775246/working/building/REAL300004918396 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918396 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918396/0 /scratch/stefan/7775246/working/building/REAL300004918396 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/398 `/scratch/stefan/7775246/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918396 none CC#CCC(NC(=O)C1CCCN1C1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 34, 51, 51, 75, 75, 75, 75, 75, 34, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 115 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44]) total number of confs: 384 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918396 none CC#CCC(NC(=O)C1CCCN1C1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 67, 27, 27, 5, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 88, 88, 115, 115, 115, 115, 115, 67, 27, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 115 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 565 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918396 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918396 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918396/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918396 Building REAL300004918397 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918397' /scratch/stefan/7775246/working/building/REAL300004918397 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918397 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918397/0 /scratch/stefan/7775246/working/building/REAL300004918397 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/399 `/scratch/stefan/7775246/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(C)=CC=C1OC)C(=O)[O-]) `REAL300004918397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918397 none CC#CCC(NC(=O)C=CC1=CC(C)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 88, 48, 49, 9, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 88, 126, 126, 180, 180, 180, 180, 180, 88, 49, 9, 9, 1, 2, 2, 2, 1, 1, 4, 4, 4] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39]) total number of confs: 892 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918397 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918397 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918397/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918397 Building REAL300004918398 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918398' /scratch/stefan/7775246/working/building/REAL300004918398 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918398 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918398/0 /scratch/stefan/7775246/working/building/REAL300004918398 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/400 `/scratch/stefan/7775246/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCNC(=O)C2)C=C1)C(=O)[O-]) `REAL300004918398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918398 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCNC(=O)C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 34, 34, 34, 34, 34, 34, 1, 1, 9, 15, 15, 33, 33, 33, 33, 33, 9, 3, 1, 1, 34, 34, 34, 34, 34, 34, 34, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 44, 43, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918398 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCNC(=O)C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 62, 62, 34, 62, 34, 34, 34, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 34, 34, 128, 164, 164, 201, 201, 201, 201, 201, 128, 62, 34, 34, 1, 1, 1, 1, 1, 1, 1, 34, 34] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 12, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44]) total number of confs: 995 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918398 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918398 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918398/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918398 Building REAL300004918399 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918399' /scratch/stefan/7775246/working/building/REAL300004918399 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918399 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918399/0 /scratch/stefan/7775246/working/building/REAL300004918399 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/401 `/scratch/stefan/7775246/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C(C)C)=CC=C1F)C(=O)[O-]) `REAL300004918399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918399 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C(C)C)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 11, 11, 1, 11, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 1, 1, 1, 1, 21, 32, 32, 44, 44, 44, 44, 44, 21, 11, 1, 18, 18, 18, 17, 18, 18, 18, 17, 17, 17, 1, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 44, 45, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918399 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918399 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918399/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918399 Building REAL300004918400 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918400' /scratch/stefan/7775246/working/building/REAL300004918400 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918400 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918400/0 /scratch/stefan/7775246/working/building/REAL300004918400 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/402 `/scratch/stefan/7775246/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC(C(C)C)=CC=C1C)C(=O)[O-]) `REAL300004918400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918400 none CC#CCC(NC(=O)C(C)OC1=CC(C(C)C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [170, 170, 170, 124, 67, 67, 16, 67, 7, 16, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 124, 137, 137, 170, 170, 170, 170, 170, 124, 67, 16, 16, 16, 16, 1, 2, 2, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2] 182 rigid atoms, others: [35, 44, 10, 11, 12, 13, 14, 17, 18, 19, 20, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 791 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918400 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918400 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918400/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918400 Building REAL300004918401 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918401' /scratch/stefan/7775246/working/building/REAL300004918401 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918401 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918401/0 /scratch/stefan/7775246/working/building/REAL300004918401 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/403 `/scratch/stefan/7775246/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC(C)=CC=C1Cl)C(=O)[O-]) `REAL300004918401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918401 none CC#CCC(NC(=O)C(C)OC1=CC(C)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 58, 58, 14, 58, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 148, 148, 201, 201, 201, 201, 201, 108, 58, 14, 14, 14, 14, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [33, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 1005 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918401 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918401 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918401/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918401 Building REAL300004918402 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918402' /scratch/stefan/7775246/working/building/REAL300004918402 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918402 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918402/0 /scratch/stefan/7775246/working/building/REAL300004918402 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/404 `/scratch/stefan/7775246/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC(C)C)C=C1)C(=O)[O-]) `REAL300004918402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918402 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 32, 36, 1, 1, 9, 13, 13, 22, 22, 22, 22, 22, 9, 3, 1, 1, 9, 27, 27, 36, 36, 36, 36, 36, 36, 36, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918402 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918402 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918402/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918402 Building REAL300004918403 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918403' /scratch/stefan/7775246/working/building/REAL300004918403 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918403 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918403/0 /scratch/stefan/7775246/working/building/REAL300004918403 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/405 `/scratch/stefan/7775246/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918403 none CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 76, 76, 22, 76, 10, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 157, 157, 201, 201, 201, 201, 201, 115, 76, 22, 22, 22, 22, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1017 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918403 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918403 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918403/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918403 Building REAL300004918404 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918404' /scratch/stefan/7775246/working/building/REAL300004918404 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918404 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918404/0 /scratch/stefan/7775246/working/building/REAL300004918404 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/406 `/scratch/stefan/7775246/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(F)C(Cl)=C1)C(=O)[O-]) `REAL300004918404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918404 none CC#CCC(NC(=O)COC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 88, 88, 18, 88, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 166, 166, 201, 201, 201, 201, 201, 129, 88, 18, 18, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 982 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918404 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918404 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918404/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918404 Building REAL300004918405 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918405' /scratch/stefan/7775246/working/building/REAL300004918405 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918405 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918405/0 /scratch/stefan/7775246/working/building/REAL300004918405 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/407 `/scratch/stefan/7775246/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-]) `REAL300004918405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918405 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 5, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 11, 11, 1, 1, 5, 7, 7, 17, 17, 17, 17, 17, 5, 3, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 1, 1] 38 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 45, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918405 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 20, 15, 15, 11, 15, 11, 11, 11, 11, 11, 11, 6, 11, 11, 1, 1, 1, 1, 11, 11, 20, 21, 21, 38, 38, 38, 38, 38, 20, 15, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 11, 11] 38 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918405 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918405 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918405/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918405 Building REAL300004918406 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918406' /scratch/stefan/7775246/working/building/REAL300004918406 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918406 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918406/0 /scratch/stefan/7775246/working/building/REAL300004918406 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/408 `/scratch/stefan/7775246/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-]) `REAL300004918406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918406 none CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 20, 11, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 20, 34, 34, 54, 54, 54, 54, 54, 20, 11, 3, 3, 1, 1, 9, 25, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 43, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 345 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918406 none CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 138, 96, 96, 38, 96, 38, 25, 25, 25, 25, 15, 5, 15, 15, 1, 1, 1, 1, 25, 25, 138, 176, 176, 201, 201, 201, 201, 201, 138, 96, 38, 38, 25, 25, 5, 1, 1, 1, 1, 1, 25, 25] 201 rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 1014 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918406 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918406 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918406/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918406 Building REAL300004918407 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918407' /scratch/stefan/7775246/working/building/REAL300004918407 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918407 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918407/0 /scratch/stefan/7775246/working/building/REAL300004918407 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/409 `/scratch/stefan/7775246/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC)C(S(=O)(=O)NCC)=C1)C(=O)[O-]) `REAL300004918407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918407 none CC#CCC(NC(=O)C=CC1=CC=C(OC)C(S(=O)(=O)NCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 38, 19, 19, 5, 19, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 5, 5, 5, 11, 24, 1, 38, 58, 58, 82, 82, 82, 82, 82, 38, 19, 5, 5, 1, 1, 4, 4, 4, 11, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 47, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 519 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918407 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918407 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918407/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918407 Building REAL300004918408 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918408' /scratch/stefan/7775246/working/building/REAL300004918408 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918408 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918408/0 /scratch/stefan/7775246/working/building/REAL300004918408 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/410 `/scratch/stefan/7775246/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918408 none CC#CCC(NC(=O)C(C)OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 115, 65, 65, 14, 65, 6, 14, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 115, 120, 120, 196, 196, 196, 196, 196, 115, 65, 14, 14, 14, 14, 1, 1, 3, 3, 1, 3, 3, 1, 1] 201 rigid atoms, others: [45, 37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 858 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918408 none CC#CCC(NC(=O)C(C)OC1=CC=C(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 167, 105, 105, 23, 105, 10, 23, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 167, 172, 172, 201, 201, 201, 201, 201, 167, 105, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 1, 3, 3] 201 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 836 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918408 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918408 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918408/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918408 Building REAL300004918409 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918409' /scratch/stefan/7775246/working/building/REAL300004918409 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918409 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918409/0 /scratch/stefan/7775246/working/building/REAL300004918409 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/411 `/scratch/stefan/7775246/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC(C)C)=CC=C1F)C(=O)[O-]) `REAL300004918409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918409 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC(C)C)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 27, 12, 12, 1, 12, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 1, 1, 1, 1, 27, 43, 43, 72, 72, 72, 72, 72, 27, 12, 1, 9, 14, 14, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 18, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918409 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918409 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918409/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918409 Building REAL300004918410 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918410' /scratch/stefan/7775246/working/building/REAL300004918410 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918410 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918410/0 /scratch/stefan/7775246/working/building/REAL300004918410 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/412 `/scratch/stefan/7775246/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918410 none CC#CCC(NC(=O)C=CC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 118, 50, 50, 6, 51, 6, 1, 1, 1, 1, 1, 1, 1, 1, 118, 149, 149, 195, 195, 195, 195, 195, 118, 51, 7, 6, 1, 1, 1, 1] 195 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 905 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918410 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918410 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918410/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918410 Building REAL300004918411 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918411' /scratch/stefan/7775246/working/building/REAL300004918411 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918411 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918411/0 /scratch/stefan/7775246/working/building/REAL300004918411 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/413 `/scratch/stefan/7775246/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC2=CC=CO2)C=C1)C(=O)[O-]) `REAL300004918411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918411 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC2=CC=CO2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 24, 47, 47, 47, 47, 1, 1, 7, 10, 10, 17, 17, 17, 17, 17, 7, 3, 1, 1, 5, 24, 24, 47, 47, 47, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918411 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC2=CC=CO2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 72, 72, 47, 72, 27, 47, 47, 27, 18, 27, 27, 3, 1, 1, 1, 1, 1, 1, 47, 47, 117, 152, 152, 201, 201, 201, 201, 201, 117, 72, 47, 47, 18, 3, 3, 1, 1, 1, 47, 47] 201 rigid atoms, others: [39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 1149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918411 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918411 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918411/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918411 Building REAL300004918412 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918412' /scratch/stefan/7775246/working/building/REAL300004918412 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918412 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918412/0 /scratch/stefan/7775246/working/building/REAL300004918412 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/414 `/scratch/stefan/7775246/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918412 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 82, 82, 20, 82, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 131, 172, 172, 201, 201, 201, 201, 201, 131, 82, 20, 20, 5, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1017 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918412 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918412 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918412/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918412 Building REAL300004918413 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918413' /scratch/stefan/7775246/working/building/REAL300004918413 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918413 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918413/0 /scratch/stefan/7775246/working/building/REAL300004918413 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/415 `/scratch/stefan/7775246/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC(=O)C1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918413 none CC#CCC(NC(=O)CCCNC(=O)C1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 23, 21, 21, 15, 21, 15, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 28, 28, 28, 28, 28, 23, 21, 15, 15, 15, 15, 14, 14, 3, 1, 1, 1, 1] 28 rigid atoms, others: [38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918413 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918413 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918413/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918413 Building REAL300004918414 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918414' /scratch/stefan/7775246/working/building/REAL300004918414 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918414 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918414/0 /scratch/stefan/7775246/working/building/REAL300004918414 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/416 `/scratch/stefan/7775246/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)C(C)=C1)C(=O)[O-]) `REAL300004918414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918414 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 31, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 1, 31, 46, 46, 62, 62, 62, 62, 62, 31, 12, 2, 2, 2, 7, 7, 1, 7, 7, 7, 7, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 45, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918414 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 52, 52, 7, 52, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 114, 142, 142, 201, 201, 201, 201, 201, 114, 52, 7, 7, 7, 1, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7] 201 rigid atoms, others: [35, 36, 37, 41, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 918 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918414 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918414 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918414/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918414 Building REAL300004918415 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918415' /scratch/stefan/7775246/working/building/REAL300004918415 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918415 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918415/0 /scratch/stefan/7775246/working/building/REAL300004918415 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/417 `/scratch/stefan/7775246/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(Cl)C=C1)C(C)CC)C(=O)[O-]) `REAL300004918415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918415 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(Cl)C=C1)C(C)CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 50, 27, 27, 7, 27, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 20, 22, 27, 50, 53, 53, 73, 73, 73, 73, 73, 50, 27, 7, 3, 1, 1, 1, 1, 22, 22, 22, 22, 27, 27, 27, 27, 27] 86 rigid atoms, others: [35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 420 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918415 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918415 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918415/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918415 Building REAL300004918416 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918416' /scratch/stefan/7775246/working/building/REAL300004918416 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918416 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918416/0 /scratch/stefan/7775246/working/building/REAL300004918416 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/418 `/scratch/stefan/7775246/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(Cl)C=C1)C(C)C)C(=O)[O-]) `REAL300004918416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918416 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(Cl)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 28, 21, 21, 5, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 28, 28, 28, 32, 32, 32, 32, 32, 28, 21, 5, 3, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14] 34 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918416 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918416 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918416/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918416 Building REAL300004918417 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918417' /scratch/stefan/7775246/working/building/REAL300004918417 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918417 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918417/0 /scratch/stefan/7775246/working/building/REAL300004918417 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/419 `/scratch/stefan/7775246/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC2=CC=CC=C2N1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918417 none CC#CCC(NC(=O)CCC1=NC2=CC=CC=C2N1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 117, 58, 58, 11, 58, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 117, 158, 158, 190, 190, 190, 190, 190, 117, 58, 11, 11, 5, 5, 1, 1, 1, 1, 4, 4, 3, 4, 4] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 1024 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918417 none CC#CCC(NC(=O)CCC1=NC2=CC=CC=C2N1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 161, 92, 92, 21, 92, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 161, 185, 185, 201, 201, 201, 201, 201, 161, 92, 21, 21, 12, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 956 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918417 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918417 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918417/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918417 Building REAL300004918418 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918418' /scratch/stefan/7775246/working/building/REAL300004918418 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918418 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918418/0 /scratch/stefan/7775246/working/building/REAL300004918418 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/420 `/scratch/stefan/7775246/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(CCCCC2)S1)C(=O)[O-]) `REAL300004918418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918418 none CC#CCC(NC(=O)C1=CC2=C(CCCCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 35, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 71, 71, 71, 71, 71, 35, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918418 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918418 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918418/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918418 Building REAL300004918419 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918419' /scratch/stefan/7775246/working/building/REAL300004918419 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918419 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918419/0 /scratch/stefan/7775246/working/building/REAL300004918419 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/421 `/scratch/stefan/7775246/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC(=O)NC1=CC=CC=C1F)C(=O)[O-]) `REAL300004918419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918419 none CC#CCC(NC(=O)C1=CC=CC=C1OCC(=O)NC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 9, 9, 5, 9, 9, 9, 5, 6, 6, 8, 8, 8, 8, 8, 5, 3, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 9] 12 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918419 none CC#CCC(NC(=O)C1=CC=CC=C1OCC(=O)NC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 12, 12, 12, 12, 11, 9, 9, 9, 9, 9, 8, 8, 5, 1, 1, 1, 1] 12 rigid atoms, others: [43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918419 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918419 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918419/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918419 Building REAL300004918420 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918420' /scratch/stefan/7775246/working/building/REAL300004918420 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918420 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918420/0 /scratch/stefan/7775246/working/building/REAL300004918420 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/422 `/scratch/stefan/7775246/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=NC(C)=CC(C)=N1)C(=O)[O-]) `REAL300004918420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918420 none CC#CCC(NC(=O)CSC1=NC(C)=CC(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 63, 36, 36, 18, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 83, 83, 111, 111, 111, 111, 111, 63, 36, 18, 18, 2, 2, 2, 1, 2, 2, 2] 111 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918420 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918420 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918420/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918420 Building REAL300004918421 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918421' /scratch/stefan/7775246/working/building/REAL300004918421 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918421 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918421/0 /scratch/stefan/7775246/working/building/REAL300004918421 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/423 `/scratch/stefan/7775246/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC2=C1CCC(C)C2)C(=O)[O-]) `REAL300004918421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918421 none CC#CCC(NC(=O)C1=CSC2=C1CCC(C)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 42, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 59, 59, 99, 99, 99, 99, 99, 42, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 99 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918421 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918421 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918421/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918421 Building REAL300004918422 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918422' /scratch/stefan/7775246/working/building/REAL300004918422 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918422 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918422/0 /scratch/stefan/7775246/working/building/REAL300004918422 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/424 `/scratch/stefan/7775246/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C)C=C1)C(=O)[O-]) `REAL300004918422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918422 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 14, 22, 22, 43, 43, 43, 43, 43, 14, 4, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1] 125 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 40, 19, 20, 41, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918422 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 62, 22, 22, 4, 22, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 62, 79, 79, 125, 125, 125, 125, 125, 62, 22, 10, 10, 2, 2, 2, 1, 2, 2, 2, 10, 10] 125 rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 591 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918422 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918422 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918422/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918422 Building REAL300004918423 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918423' /scratch/stefan/7775246/working/building/REAL300004918423 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918423 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918423/0 /scratch/stefan/7775246/working/building/REAL300004918423 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/425 `/scratch/stefan/7775246/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CCSC)NC(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918423 none CC#CCC(NC(=O)C(CCSC)NC(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 51, 33, 33, 7, 33, 3, 7, 23, 32, 82, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 51, 51, 94, 94, 94, 94, 94, 51, 33, 7, 25, 25, 32, 30, 82, 82, 82, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918423 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918423 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918423/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918423 Building REAL300004918424 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918424' /scratch/stefan/7775246/working/building/REAL300004918424 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918424 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918424/0 /scratch/stefan/7775246/working/building/REAL300004918424 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/426 `/scratch/stefan/7775246/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(CC2=CC=CC=C2)C(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918424 none CC#CCC(NC(=O)C1=NN(CC2=CC=CC=C2)C(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', '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.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 29, 9, 9, 1, 9, 1, 1, 1, 1, 5, 14, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 29, 46, 46, 66, 66, 66, 66, 66, 29, 9, 5, 5, 14, 14, 13, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [43, 6, 8, 9, 10, 11, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918424 none CC#CCC(NC(=O)C1=NN(CC2=CC=CC=C2)C(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', '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.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 134, 62, 62, 14, 62, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 134, 168, 168, 201, 201, 201, 201, 201, 134, 62, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [38, 39, 40, 41, 42, 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, 43, 44, 45, 46]) total number of confs: 974 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918424 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918424 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918424/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918424 Building REAL300004918425 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918425' /scratch/stefan/7775246/working/building/REAL300004918425 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918425 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918425/0 /scratch/stefan/7775246/working/building/REAL300004918425 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/427 `/scratch/stefan/7775246/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(C)C=C1)C(C)C)C(=O)[O-]) `REAL300004918425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918425 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(C)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 46, 30, 30, 7, 30, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 46, 47, 47, 62, 62, 62, 62, 62, 46, 30, 7, 3, 1, 1, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20] 72 rigid atoms, others: [34, 35, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 323 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918425 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918425 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918425/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918425 Building REAL300004918426 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918426' /scratch/stefan/7775246/working/building/REAL300004918426 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918426 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918426/0 /scratch/stefan/7775246/working/building/REAL300004918426 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/428 `/scratch/stefan/7775246/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(C(C)(C)C)C=C1)C(C)C)C(=O)[O-]) `REAL300004918426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918426 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(C(C)(C)C)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 31, 19, 19, 5, 19, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 14, 14, 31, 31, 31, 47, 47, 47, 47, 47, 31, 19, 5, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [48, 37, 38, 10, 12, 13, 14, 15, 16, 49, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 283 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918426 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918426 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918426/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918426 Building REAL300004918427 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918427' /scratch/stefan/7775246/working/building/REAL300004918427 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918427 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918427/0 /scratch/stefan/7775246/working/building/REAL300004918427 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/429 `/scratch/stefan/7775246/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(OCC)C=C1)C(=O)[O-]) `REAL300004918427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918427 none CC#CCC(NC(=O)CCCOC1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 52, 38, 38, 19, 38, 15, 5, 3, 1, 1, 1, 1, 1, 1, 6, 15, 1, 1, 52, 71, 71, 105, 105, 105, 105, 105, 52, 38, 19, 19, 15, 15, 5, 5, 1, 1, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [45, 37, 38, 44, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 566 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918427 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918427 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918427/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918427 Building REAL300004918428 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918428' /scratch/stefan/7775246/working/building/REAL300004918428 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918428 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918428/0 /scratch/stefan/7775246/working/building/REAL300004918428 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/430 `/scratch/stefan/7775246/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC=C(Cl)C=C2)C1)C(=O)[O-]) `REAL300004918428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918428 none CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC=C(Cl)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 33, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 1, 33, 52, 52, 92, 92, 92, 92, 92, 33, 12, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 22, 45, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43]) total number of confs: 475 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918428 none CC#CCC(NC(=O)C1CCCN(C(=O)C2=CC=C(Cl)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 74, 74, 14, 74, 14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 14, 139, 163, 163, 201, 201, 201, 201, 201, 139, 74, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14] 201 rigid atoms, others: [40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 916 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918428 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918428 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918428/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918428 Building REAL300004918429 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918429' /scratch/stefan/7775246/working/building/REAL300004918429 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918429 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918429/0 /scratch/stefan/7775246/working/building/REAL300004918429 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/431 `/scratch/stefan/7775246/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC1CC1)C(=O)[O-]) `REAL300004918429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918429 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 22, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 9, 31, 67, 67, 22, 36, 36, 52, 52, 52, 52, 52, 22, 11, 1, 1, 1, 1, 31, 31, 67, 67, 67, 67, 67] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918429 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 137, 111, 111, 67, 111, 67, 67, 67, 67, 67, 35, 8, 1, 1, 1, 1, 137, 162, 162, 201, 201, 201, 201, 201, 137, 111, 67, 67, 67, 67, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918429 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918429 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918429/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918429 Building REAL300004918430 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918430' /scratch/stefan/7775246/working/building/REAL300004918430 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918430 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918430/0 /scratch/stefan/7775246/working/building/REAL300004918430 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/432 `/scratch/stefan/7775246/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC(Br)=CS2)=N1)C(=O)[O-]) `REAL300004918430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918430 none CC#CCC(NC(=O)C1=CSC(C2=CC(Br)=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 17, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 13, 12, 13, 12, 13, 1, 31, 47, 47, 84, 84, 84, 84, 84, 31, 11, 1, 13, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918430 none CC#CCC(NC(=O)C1=CSC(C2=CC(Br)=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 17, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 58, 58, 13, 58, 12, 12, 13, 1, 1, 1, 1, 1, 1, 1, 12, 115, 148, 148, 201, 201, 201, 201, 201, 115, 58, 12, 1, 1] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 921 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918430 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918430 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918430/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918430 Building REAL300004918431 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918431' /scratch/stefan/7775246/working/building/REAL300004918431 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918431 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918431/0 /scratch/stefan/7775246/working/building/REAL300004918431 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/433 `/scratch/stefan/7775246/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OC)C(OC)=C1OC)C(=O)[O-]) `REAL300004918431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918431 none CC#CCC(NC(=O)CCC1=CC=C(OC)C(OC)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 4, 5, 5, 5, 4, 4, 4] 8 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918431 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918431 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918431/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918431 Building REAL300004918432 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918432' /scratch/stefan/7775246/working/building/REAL300004918432 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918432 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918432/0 /scratch/stefan/7775246/working/building/REAL300004918432 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/434 `/scratch/stefan/7775246/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC=C1F)C(=O)[O-]) `REAL300004918432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918432 none CC#CCC(NC(=O)CCCOC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 109, 109, 51, 109, 48, 32, 10, 1, 1, 1, 1, 1, 1, 1, 1, 131, 158, 158, 201, 201, 201, 201, 201, 131, 109, 51, 51, 47, 47, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1006 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918432 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918432 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918432/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918432 Building REAL300004918433 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918433' /scratch/stefan/7775246/working/building/REAL300004918433 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918433 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918433/0 /scratch/stefan/7775246/working/building/REAL300004918433 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/435 `/scratch/stefan/7775246/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2=CC=C(C)C(F)=C2)=NO1)C(=O)[O-]) `REAL300004918433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918433 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(C)C(F)=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 15, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 98, 72, 72, 19, 71, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 98, 124, 124, 126, 126, 126, 126, 126, 98, 72, 19, 19, 8, 8, 4, 4, 5, 5, 5, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918433 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(C)C(F)=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 15, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 134, 134, 52, 133, 30, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 169, 200, 200, 201, 201, 201, 201, 201, 169, 134, 53, 53, 30, 30, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [37, 38, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 977 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918433 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918433 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918433/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918433 Building REAL300004918434 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918434' /scratch/stefan/7775246/working/building/REAL300004918434 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918434 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918434/0 /scratch/stefan/7775246/working/building/REAL300004918434 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/436 `/scratch/stefan/7775246/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2=CC=C(F)C(C)=C2)=NO1)C(=O)[O-]) `REAL300004918434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918434 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(F)C(C)=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 92, 66, 66, 19, 66, 8, 1, 1, 1, 1, 1, 5, 5, 2, 2, 5, 5, 5, 1, 1, 92, 113, 113, 113, 113, 113, 113, 113, 92, 67, 19, 19, 8, 8, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [9, 10, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918434 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(F)C(C)=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 136, 136, 54, 136, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 173, 201, 201, 201, 201, 201, 201, 201, 173, 136, 54, 54, 30, 30, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [37, 38, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 961 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918434 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918434 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918434/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918434 Building REAL300004918435 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918435' /scratch/stefan/7775246/working/building/REAL300004918435 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918435 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918435/0 /scratch/stefan/7775246/working/building/REAL300004918435 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/437 `/scratch/stefan/7775246/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)NC2CC2)=C1)C(=O)[O-]) `REAL300004918435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918435 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)NC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 26, 26, 1, 13, 21, 21, 39, 39, 39, 39, 39, 13, 5, 1, 1, 1, 7, 9, 26, 26, 26, 26, 26, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 20, 41, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918435 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)NC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 61, 61, 26, 61, 26, 26, 26, 26, 12, 8, 6, 8, 1, 1, 1, 1, 26, 105, 142, 142, 201, 201, 201, 201, 201, 105, 61, 26, 26, 26, 12, 6, 1, 1, 1, 1, 1, 26] 201 rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 975 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918435 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918435 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918435/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918435 Building REAL300004918436 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918436' /scratch/stefan/7775246/working/building/REAL300004918436 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918436 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918436/0 /scratch/stefan/7775246/working/building/REAL300004918436 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/438 `/scratch/stefan/7775246/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=O)N(CC)S(=O)(=O)C2=C1)C(=O)[O-]) `REAL300004918436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918436 none CC#CCC(NC(=O)C1=CC=C2C(=O)N(CC)S(=O)(=O)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 14, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 29, 41, 41, 67, 67, 67, 67, 67, 29, 7, 1, 1, 3, 3, 3, 3, 3, 1] 130 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918436 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918436 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918436/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918436 Building REAL300004918437 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918437' /scratch/stefan/7775246/working/building/REAL300004918437 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918437 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918437/0 /scratch/stefan/7775246/working/building/REAL300004918437 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/439 `/scratch/stefan/7775246/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)NC1CCCCC1)C(=O)[O-]) `REAL300004918437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918437 none CC#CCC(NC(=O)CNC(=O)NC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 133, 78, 78, 34, 78, 12, 9, 7, 9, 1, 1, 1, 1, 1, 1, 1, 133, 173, 173, 201, 201, 201, 201, 201, 133, 78, 34, 34, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: 1063 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918437 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918437 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918437/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918437 Building REAL300004918438 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918438' /scratch/stefan/7775246/working/building/REAL300004918438 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918438 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918438/0 /scratch/stefan/7775246/working/building/REAL300004918438 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/440 `/scratch/stefan/7775246/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CN1CC1=CC=CS1)C(=O)[O-]) `REAL300004918438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918438 none CC#CCC(NC(=O)C1=CC=CN1CC1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 25, 42, 42, 66, 66, 66, 66, 66, 25, 10, 1, 1, 1, 6, 6, 15, 15, 15] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918438 none CC#CCC(NC(=O)C1=CC=CN1CC1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 52, 52, 15, 52, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 102, 148, 148, 201, 201, 201, 201, 201, 102, 52, 15, 15, 15, 4, 4, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1011 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918438 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918438 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918438/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918438 Building REAL300004918439 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918439' /scratch/stefan/7775246/working/building/REAL300004918439 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918439 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918439/0 /scratch/stefan/7775246/working/building/REAL300004918439 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/441 `/scratch/stefan/7775246/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)NCC1=CC=CO1)C(=O)[O-]) `REAL300004918439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918439 none CC#CCC(NC(=O)CNC(=O)NCC1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 140, 96, 96, 55, 96, 23, 19, 17, 19, 5, 1, 1, 1, 1, 1, 1, 140, 183, 183, 201, 201, 201, 201, 201, 140, 96, 55, 55, 23, 17, 5, 5, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1110 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918439 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918439 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918439/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918439 Building REAL300004918440 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918440' /scratch/stefan/7775246/working/building/REAL300004918440 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918440 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918440/0 /scratch/stefan/7775246/working/building/REAL300004918440 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/442 `/scratch/stefan/7775246/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(OC(F)(F)F)C=CC=C2N1)C(=O)[O-]) `REAL300004918440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918440 none CC#CCC(NC(=O)C1=CC2=C(OC(F)(F)F)C=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [71, 71, 71, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1, 1, 1, 1, 1, 24, 40, 40, 71, 71, 71, 71, 71, 24, 8, 1, 1, 1, 1, 1] 169 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918440 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918440 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918440/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918440 Building REAL300004918441 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918441' /scratch/stefan/7775246/working/building/REAL300004918441 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918441 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918441/0 /scratch/stefan/7775246/working/building/REAL300004918441 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/443 `/scratch/stefan/7775246/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(C2=CC=CC=C2)N=N1)C(=O)[O-]) `REAL300004918441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918441 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 70, 30, 29, 6, 30, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 70, 106, 106, 162, 162, 162, 162, 162, 70, 29, 6, 6, 2, 2, 2, 3, 3, 2, 3, 3] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918441 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 55, 55, 13, 55, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 114, 154, 154, 201, 201, 201, 201, 201, 114, 55, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1024 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918441 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918441 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918441/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918441 Building REAL300004918442 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918442' /scratch/stefan/7775246/working/building/REAL300004918442 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918442 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918442/0 /scratch/stefan/7775246/working/building/REAL300004918442 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/444 `/scratch/stefan/7775246/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)N=N1)C(=O)[O-]) `REAL300004918442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918442 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 42, 12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 42, 62, 62, 103, 103, 103, 103, 103, 42, 12, 2, 2, 2, 3, 3, 2, 3, 3] 125 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 498 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918442 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 67, 23, 23, 3, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 67, 88, 88, 125, 125, 125, 125, 125, 67, 23, 3, 3, 3, 1, 1, 1, 1, 1] 125 rigid atoms, others: [33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 579 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918442 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918442 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918442/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918442 Building REAL300004918443 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918443' /scratch/stefan/7775246/working/building/REAL300004918443 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918443 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918443/0 /scratch/stefan/7775246/working/building/REAL300004918443 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/445 `/scratch/stefan/7775246/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(C)C=C2)N=N1)C(=O)[O-]) `REAL300004918443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918443 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(C)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 39, 60, 60, 94, 94, 94, 94, 94, 39, 12, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 117 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 484 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918443 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(C)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 66, 23, 23, 4, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 66, 87, 87, 117, 117, 117, 117, 117, 66, 23, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1] 117 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 566 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918443 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918443 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918443/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918443 Building REAL300004918444 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918444' /scratch/stefan/7775246/working/building/REAL300004918444 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918444 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918444/0 /scratch/stefan/7775246/working/building/REAL300004918444 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/446 `/scratch/stefan/7775246/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=CC=C1Br)C(=O)[O-]) `REAL300004918444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918444 none CC#CCC(NC(=O)CC(C)C1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 61, 61, 15, 61, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 115, 144, 144, 201, 201, 201, 201, 201, 115, 61, 15, 15, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 969 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918444 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918444 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918444/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918444 Building REAL300004918445 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918445' /scratch/stefan/7775246/working/building/REAL300004918445 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918445 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918445/0 /scratch/stefan/7775246/working/building/REAL300004918445 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/447 `/scratch/stefan/7775246/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCN1C(=O)C1=CC=CO1)C(=O)[O-]) `REAL300004918445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918445 none CC#CCC(NC(=O)C1CCCCN1C(=O)C1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 15, 23, 23, 42, 42, 42, 42, 42, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 70 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38, 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, 40, 41, 42]) total number of confs: 205 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918445 none CC#CCC(NC(=O)C1CCCCN1C(=O)C1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 41, 20, 20, 10, 20, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 41, 52, 52, 70, 70, 70, 70, 70, 41, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1] 70 rigid atoms, others: [40, 41, 42, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 328 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918445 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918445 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918445/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918445 Building REAL300004918446 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918446' /scratch/stefan/7775246/working/building/REAL300004918446 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918446 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918446/0 /scratch/stefan/7775246/working/building/REAL300004918446 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/448 `/scratch/stefan/7775246/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC(=O)N1CC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918446 none CC#CCC(NC(=O)C1CCC(=O)N1CC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 34, 52, 52, 80, 80, 80, 80, 80, 34, 10, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 413 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918446 none CC#CCC(NC(=O)C1CCC(=O)N1CC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 49, 49, 11, 49, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 109, 151, 151, 201, 201, 201, 201, 201, 109, 49, 11, 11, 11, 11, 11, 5, 5, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 1003 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918446 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918446 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918446/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918446 Building REAL300004918447 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918447' /scratch/stefan/7775246/working/building/REAL300004918447 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918447 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918447/0 /scratch/stefan/7775246/working/building/REAL300004918447 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/449 `/scratch/stefan/7775246/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CCC1=CC=CC(F)=C1)C(=O)[O-]) `REAL300004918447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918447 none CC#CCC(NC(=O)C(C)CCC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 68, 68, 19, 68, 7, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 128, 169, 169, 201, 201, 201, 201, 201, 128, 68, 19, 19, 19, 19, 7, 7, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1021 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918447 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918447 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918447/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918447 Building REAL300004918448 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918448' /scratch/stefan/7775246/working/building/REAL300004918448 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918448 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918448/0 /scratch/stefan/7775246/working/building/REAL300004918448 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/450 `/scratch/stefan/7775246/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC2=CC(C)=C(C)C=C2O1)C(=O)[O-]) `REAL300004918448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918448 none CC#CCC(NC(=O)C1CC2=CC(C)=C(C)C=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 44, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 66, 66, 107, 107, 107, 107, 107, 44, 13, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 107 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 523 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918448 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918448 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918448/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918448 Building REAL300004918449 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918449' /scratch/stefan/7775246/working/building/REAL300004918449 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918449 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918449/0 /scratch/stefan/7775246/working/building/REAL300004918449 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/451 `/scratch/stefan/7775246/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=CC=C(Br)S1)C(=O)[O-]) `REAL300004918449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918449 none CC#CCC(NC(=O)C(C)C1=CC=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 59, 59, 11, 59, 1, 11, 1, 1, 1, 1, 1, 1, 112, 149, 149, 201, 201, 201, 201, 201, 112, 59, 11, 12, 12, 12, 1, 1] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 967 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918449 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918449 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918449/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918449 Building REAL300004918450 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918450' /scratch/stefan/7775246/working/building/REAL300004918450 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918450 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918450/0 /scratch/stefan/7775246/working/building/REAL300004918450 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/452 `/scratch/stefan/7775246/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OCCC)C=C1)C(=O)[O-]) `REAL300004918450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918450 none CC#CCC(NC(=O)CCC1=CC=C(OCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 19, 10, 10, 2, 10, 2, 1, 1, 1, 1, 1, 1, 6, 7, 15, 1, 1, 19, 35, 35, 63, 63, 63, 63, 63, 19, 10, 2, 2, 2, 2, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 44, 43, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918450 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918450 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918450/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918450 Building REAL300004918451 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918451' /scratch/stefan/7775246/working/building/REAL300004918451 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918451 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918451/0 /scratch/stefan/7775246/working/building/REAL300004918451 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/453 `/scratch/stefan/7775246/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=C(C)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918451 none CC#CCC(NC(=O)C=C(C)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 70, 70, 11, 70, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 154, 154, 201, 201, 201, 201, 201, 121, 70, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 917 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918451 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918451 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918451/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918451 Building REAL300004918452 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918452' /scratch/stefan/7775246/working/building/REAL300004918452 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918452 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918452/0 /scratch/stefan/7775246/working/building/REAL300004918452 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/454 `/scratch/stefan/7775246/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)(CC)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918452 none CC#CCC(NC(=O)C(CC)(CC)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 45, 24, 24, 6, 24, 1, 6, 8, 6, 7, 1, 1, 1, 1, 1, 1, 45, 61, 61, 84, 84, 84, 84, 84, 45, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1] 90 rigid atoms, others: [17, 39, 8, 41, 42, 43, 13, 14, 15, 16, 40, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 465 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918452 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918452 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918452/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918452 Building REAL300004918453 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918453' /scratch/stefan/7775246/working/building/REAL300004918453 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918453 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918453/0 /scratch/stefan/7775246/working/building/REAL300004918453 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/455 `/scratch/stefan/7775246/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CC)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918453 none CC#CCC(NC(=O)C1=CC=C(CC)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 1, 1, 2, 2, 1, 26, 44, 44, 90, 90, 90, 90, 90, 26, 7, 1, 1, 4, 4, 4, 4, 4, 1] 132 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 14, 15, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918453 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918453 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918453/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918453 Building REAL300004918454 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918454' /scratch/stefan/7775246/working/building/REAL300004918454 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918454 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918454/0 /scratch/stefan/7775246/working/building/REAL300004918454 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/456 `/scratch/stefan/7775246/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CCOC1=CC=CC=C1)C(=O)[O-]) `REAL300004918454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918454 none CC#CCC(NC(=O)C(C)CCOC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 81, 81, 29, 81, 17, 29, 9, 3, 1, 1, 1, 1, 1, 1, 1, 133, 182, 182, 201, 201, 201, 201, 201, 133, 81, 29, 29, 29, 29, 16, 16, 9, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1109 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918454 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918454 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918454/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918454 Building REAL300004918455 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918455' /scratch/stefan/7775246/working/building/REAL300004918455 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918455 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918455/0 /scratch/stefan/7775246/working/building/REAL300004918455 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/457 `/scratch/stefan/7775246/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC(C)=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918455 none CC#CCC(NC(=O)C1=CC(F)=CC(C)=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 5, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 26, 26, 45, 45, 45, 45, 45, 17, 6, 1, 1, 2, 2, 2] 45 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918455 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918455 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918455/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918455 Building REAL300004918456 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918456' /scratch/stefan/7775246/working/building/REAL300004918456 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918456 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918456/0 /scratch/stefan/7775246/working/building/REAL300004918456 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/458 `/scratch/stefan/7775246/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)OC1=CC=CC=C1F)C(=O)[O-]) `REAL300004918456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918456 none CC#CCC(NC(=O)C(CC)OC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 78, 46, 46, 13, 46, 6, 13, 22, 1, 1, 1, 1, 1, 1, 1, 1, 78, 119, 119, 158, 158, 158, 158, 158, 78, 46, 13, 25, 25, 25, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 902 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918456 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918456 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918456/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918456 Building REAL300004918457 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918457' /scratch/stefan/7775246/working/building/REAL300004918457 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918457 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918457/0 /scratch/stefan/7775246/working/building/REAL300004918457 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/459 `/scratch/stefan/7775246/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2CCCC2)S1)C(=O)[O-]) `REAL300004918457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918457 none CC#CCC(NC(=O)C1=C(C)N=C(C2CCCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 31, 45, 45, 66, 66, 66, 66, 66, 31, 10, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918457 none CC#CCC(NC(=O)C1=C(C)N=C(C2CCCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 65, 65, 13, 65, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 136, 164, 164, 201, 201, 201, 201, 201, 136, 65, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 903 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918457 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918457 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918457/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918457 Building REAL300004918458 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918458' /scratch/stefan/7775246/working/building/REAL300004918458 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918458 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918458/0 /scratch/stefan/7775246/working/building/REAL300004918458 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/460 `/scratch/stefan/7775246/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CN(CC2=NC3=CC=CC=C3C(=O)N2)CCO1)C(=O)[O-]) `REAL300004918458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918458 none CC#CCC(NC(=O)C1CN(CC2=NC3=CC=CC=C3C(=O)N2)CCO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 27, 12, 12, 1, 12, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 27, 47, 47, 69, 69, 69, 69, 69, 27, 12, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 46, 47, 48, 49, 23, 24, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918458 none CC#CCC(NC(=O)C1CN(CC2=NC3=CC=CC=C3C(=O)N2)CCO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 74, 74, 14, 74, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 132, 163, 163, 201, 201, 201, 201, 201, 132, 74, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49]) total number of confs: 975 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918458 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918458 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918458/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918458 Building REAL300004918459 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918459' /scratch/stefan/7775246/working/building/REAL300004918459 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918459 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918459/0 /scratch/stefan/7775246/working/building/REAL300004918459 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/461 `/scratch/stefan/7775246/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CC(OC(C)C)=C1)C(=O)[O-]) `REAL300004918459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918459 none CC#CCC(NC(=O)C1=CC(Br)=CC(OC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 1, 17, 27, 27, 55, 55, 55, 55, 55, 17, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 14, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918459 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918459 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918459/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918459 Building REAL300004918460 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918460' /scratch/stefan/7775246/working/building/REAL300004918460 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918460 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918460/0 /scratch/stefan/7775246/working/building/REAL300004918460 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/462 `/scratch/stefan/7775246/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(OC)C(Br)=C(C)S1)C(=O)[O-]) `REAL300004918460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918460 none CC#CCC(NC(=O)C1=C(OC)C(Br)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'Br', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 1, 17, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 49, 12, 12, 1, 12, 1, 1, 1, 4, 1, 1, 1, 1, 1, 49, 77, 77, 120, 120, 120, 120, 120, 49, 12, 5, 5, 5, 1, 1, 1] 151 rigid atoms, others: [32, 6, 8, 9, 10, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 600 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918460 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918460 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918460/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918460 Building REAL300004918461 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918461' /scratch/stefan/7775246/working/building/REAL300004918461 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918461 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918461/0 /scratch/stefan/7775246/working/building/REAL300004918461 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/463 `/scratch/stefan/7775246/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C=CC=C1OC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918461 none CC#CCC(NC(=O)C1=C(Cl)C=CC=C1OC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 9, 14, 14, 14, 25, 40, 40, 73, 73, 73, 73, 73, 25, 6, 1, 1, 1, 14, 14, 11, 14] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 373 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918461 none CC#CCC(NC(=O)C1=C(Cl)C=CC=C1OC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 94, 45, 45, 14, 45, 14, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 94, 136, 136, 201, 201, 201, 201, 201, 94, 45, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 984 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918461 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918461 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918461/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918461 Building REAL300004918462 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918462' /scratch/stefan/7775246/working/building/REAL300004918462 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918462 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918462/0 /scratch/stefan/7775246/working/building/REAL300004918462 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/464 `/scratch/stefan/7775246/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=C(OC)C=C2)S1)C(=O)[O-]) `REAL300004918462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918462 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C(OC)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 44, 12, 13, 1, 12, 1, 1, 1, 1, 1, 3, 3, 2, 2, 6, 3, 3, 1, 44, 68, 68, 116, 116, 116, 116, 116, 44, 13, 1, 3, 3, 7, 7, 7, 3, 3] 161 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918462 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C(OC)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 82, 36, 36, 3, 36, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 3, 82, 109, 109, 140, 140, 140, 140, 140, 82, 36, 3, 1, 1, 3, 3, 3, 1, 1] 161 rigid atoms, others: [32, 33, 37, 38, 11, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918462 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918462 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918462/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918462 Building REAL300004918463 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918463' /scratch/stefan/7775246/working/building/REAL300004918463 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918463 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918463/0 /scratch/stefan/7775246/working/building/REAL300004918463 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/465 `/scratch/stefan/7775246/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)N1N=NC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918463 none CC#CCC(NC(=O)C(C)N1N=NC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 108, 57, 57, 13, 57, 1, 13, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 108, 152, 152, 198, 198, 198, 198, 198, 108, 57, 13, 13, 13, 13, 4, 3, 1, 3, 3] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1024 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918463 none CC#CCC(NC(=O)C(C)N1N=NC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 90, 90, 30, 90, 3, 30, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 133, 171, 171, 201, 201, 201, 201, 201, 133, 90, 30, 30, 30, 30, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 993 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918463 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918463 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918463/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918463 Building REAL300004918464 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918464' /scratch/stefan/7775246/working/building/REAL300004918464 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918464 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918464/0 /scratch/stefan/7775246/working/building/REAL300004918464 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/466 `/scratch/stefan/7775246/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OCCC)C(=O)[O-]) `REAL300004918464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918464 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OCCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 25, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 49, 25, 41, 41, 70, 70, 70, 70, 70, 25, 12, 1, 1, 1, 31, 31, 56, 56, 56, 56, 56] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 601 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918464 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918464 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918464/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918464 Building REAL300004918465 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918465' /scratch/stefan/7775246/working/building/REAL300004918465 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918465 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918465/0 /scratch/stefan/7775246/working/building/REAL300004918465 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/467 `/scratch/stefan/7775246/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(CC)C=C2)O1)C(=O)[O-]) `REAL300004918465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918465 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(CC)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 7, 7, 1, 1, 13, 7, 7, 1, 26, 41, 41, 58, 58, 58, 58, 58, 26, 10, 1, 1, 7, 7, 13, 13, 13, 13, 13, 7, 7] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918465 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(CC)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 82, 42, 42, 7, 42, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 82, 99, 99, 132, 132, 132, 132, 132, 82, 42, 7, 7, 1, 1, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [33, 34, 40, 41, 11, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918465 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918465 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918465/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918465 Building REAL300004918466 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918466' /scratch/stefan/7775246/working/building/REAL300004918466 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918466 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918466/0 /scratch/stefan/7775246/working/building/REAL300004918466 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/468 `/scratch/stefan/7775246/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC([N+](=O)[O-])=C1Br)C(=O)[O-]) `REAL300004918466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918466 none CC#CCC(NC(=O)C1=CC(F)=CC([N+](=O)[O-])=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 38, 38, 65, 65, 65, 65, 65, 26, 7, 1, 1] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918466 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918466 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918466/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918466 Building REAL300004918467 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918467' /scratch/stefan/7775246/working/building/REAL300004918467 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918467 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918467/0 /scratch/stefan/7775246/working/building/REAL300004918467 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/469 `/scratch/stefan/7775246/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=C(C)NC1=O)C(=O)[O-]) `REAL300004918467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918467 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=C(C)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 47, 13, 13, 1, 13, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 1, 1, 47, 67, 67, 111, 111, 111, 111, 111, 47, 13, 1, 4, 4, 2, 4, 4, 2, 2, 2, 1] 111 rigid atoms, others: [32, 6, 8, 9, 10, 11, 17, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918467 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=C(C)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 59, 23, 23, 4, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 59, 77, 77, 111, 111, 111, 111, 111, 59, 23, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4] 111 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39, 40, 41]) total number of confs: 517 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918467 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918467 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918467/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918467 Building REAL300004918468 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918468' /scratch/stefan/7775246/working/building/REAL300004918468 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918468 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918468/0 /scratch/stefan/7775246/working/building/REAL300004918468 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/470 `/scratch/stefan/7775246/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC(F)F)C(=O)[O-]) `REAL300004918468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918468 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 5] 5 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918468 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918468 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918468/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918468 Building REAL300004918469 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918469' /scratch/stefan/7775246/working/building/REAL300004918469 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918469 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918469/0 /scratch/stefan/7775246/working/building/REAL300004918469 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/471 `/scratch/stefan/7775246/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN(C)C1=CC=CC=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918469 none CC#CCC(NC(=O)CN(C)C1=CC=CC=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 56, 56, 16, 56, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 112, 152, 152, 201, 201, 201, 201, 201, 112, 56, 16, 16, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1024 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918469 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918469 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918469/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918469 Building REAL300004918470 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918470' /scratch/stefan/7775246/working/building/REAL300004918470 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918470 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918470/0 /scratch/stefan/7775246/working/building/REAL300004918470 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/472 `/scratch/stefan/7775246/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918470 none CC#CCC(NC(=O)C(C)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 52, 51, 12, 51, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 104, 143, 143, 201, 201, 201, 201, 201, 104, 51, 12, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 968 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918470 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918470 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918470/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918470 Building REAL300004918471 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918471' /scratch/stefan/7775246/working/building/REAL300004918471 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918471 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918471/0 /scratch/stefan/7775246/working/building/REAL300004918471 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/473 `/scratch/stefan/7775246/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NCC)C=C1)C(=O)[O-]) `REAL300004918471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918471 none CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 27, 13, 13, 3, 13, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 20, 1, 1, 27, 43, 43, 57, 57, 57, 57, 57, 27, 13, 3, 3, 1, 1, 8, 20, 20, 20, 20, 20, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 43, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 358 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918471 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918471 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918471/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918471 Building REAL300004918472 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918472' /scratch/stefan/7775246/working/building/REAL300004918472 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918472 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918472/0 /scratch/stefan/7775246/working/building/REAL300004918472 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/474 `/scratch/stefan/7775246/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NCC)=CC=C1F)C(=O)[O-]) `REAL300004918472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918472 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NCC)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 30, 11, 11, 1, 11, 1, 1, 1, 1, 2, 2, 2, 7, 21, 1, 1, 1, 1, 30, 46, 46, 74, 74, 74, 74, 74, 30, 11, 1, 7, 21, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918472 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918472 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918472/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918472 Building REAL300004918473 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918473' /scratch/stefan/7775246/working/building/REAL300004918473 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918473 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918473/0 /scratch/stefan/7775246/working/building/REAL300004918473 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/475 `/scratch/stefan/7775246/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C2=C1CCCCC2)C(=O)[O-]) `REAL300004918473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918473 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C2=C1CCCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 36, 10, 10, 1, 10, 1, 1, 1, 1, 5, 5, 3, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 36, 55, 55, 104, 104, 104, 104, 104, 36, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 124 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 493 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918473 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C2=C1CCCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 66, 26, 26, 5, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 66, 86, 86, 124, 124, 124, 124, 124, 66, 26, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 124 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918473 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918473 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918473/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918473 Building REAL300004918474 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918474' /scratch/stefan/7775246/working/building/REAL300004918474 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918474 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918474/0 /scratch/stefan/7775246/working/building/REAL300004918474 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/476 `/scratch/stefan/7775246/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004918474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918474 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 36, 11, 11, 1, 11, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 1, 1, 1, 1, 36, 50, 50, 79, 79, 79, 79, 79, 36, 11, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1] 187 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 40, 18, 19, 20, 21, 22, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918474 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 105, 46, 46, 10, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 105, 134, 134, 187, 187, 187, 187, 187, 105, 46, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10] 187 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 864 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918474 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918474 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918474/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918474 Building REAL300004918475 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918475' /scratch/stefan/7775246/working/building/REAL300004918475 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918475 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918475/0 /scratch/stefan/7775246/working/building/REAL300004918475 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/477 `/scratch/stefan/7775246/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C2=C1CCC2)C(=O)[O-]) `REAL300004918475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918475 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 37, 12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 1, 1, 1, 1, 37, 56, 56, 103, 103, 103, 103, 103, 37, 12, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 112 rigid atoms, others: [43, 6, 8, 9, 10, 11, 44, 45, 40, 18, 19, 20, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918475 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 69, 34, 34, 6, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 69, 86, 86, 112, 112, 112, 112, 112, 69, 34, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6] 112 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918475 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918475 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918475/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918475 Building REAL300004918476 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918476' /scratch/stefan/7775246/working/building/REAL300004918476 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918476 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918476/0 /scratch/stefan/7775246/working/building/REAL300004918476 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/478 `/scratch/stefan/7775246/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C(C)(C)C)C=C2)CC1)C(=O)[O-]) `REAL300004918476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918476 none CC#CCC(NC(=O)C1(C2=CC=C(C(C)(C)C)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 40, 13, 13, 1, 13, 1, 1, 5, 5, 5, 5, 12, 12, 12, 5, 5, 1, 1, 40, 71, 71, 112, 112, 112, 112, 112, 40, 13, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [6, 8, 9, 44, 45, 46, 47, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 606 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918476 none CC#CCC(NC(=O)C1(C2=CC=C(C(C)(C)C)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 58, 26, 26, 5, 26, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 5, 5, 58, 92, 92, 139, 139, 139, 139, 139, 58, 26, 1, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 17, 18, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 713 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918476 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918476 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918476/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918476 Building REAL300004918477 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918477' /scratch/stefan/7775246/working/building/REAL300004918477 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918477 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918477/0 /scratch/stefan/7775246/working/building/REAL300004918477 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/479 `/scratch/stefan/7775246/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC(C)=CC(C)=C2)CCC1)C(=O)[O-]) `REAL300004918477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918477 none CC#CCC(NC(=O)C1(C2=CC(C)=CC(C)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 5, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 48, 12, 12, 1, 12, 1, 1, 7, 7, 7, 1, 7, 7, 7, 1, 1, 1, 48, 73, 73, 127, 127, 127, 127, 127, 48, 12, 7, 7, 7, 7, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 191 rigid atoms, others: [6, 39, 8, 9, 42, 43, 44, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 599 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918477 none CC#CCC(NC(=O)C1(C2=CC(C)=CC(C)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 5, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 100, 42, 42, 11, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 100, 133, 133, 192, 192, 192, 192, 192, 100, 42, 1, 2, 2, 2, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11] 192 rigid atoms, others: [34, 38, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 911 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918477 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918477 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918477/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918477 Building REAL300004918478 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918478' /scratch/stefan/7775246/working/building/REAL300004918478 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918478 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918478/0 /scratch/stefan/7775246/working/building/REAL300004918478 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/480 `/scratch/stefan/7775246/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=COC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918478 none CC#CCC(NC(=O)CSCC1=COC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 143, 85, 85, 45, 85, 26, 6, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 143, 167, 167, 201, 201, 201, 201, 201, 143, 85, 45, 45, 6, 6, 1, 4, 4, 2, 4, 4] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 1002 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918478 none CC#CCC(NC(=O)CSCC1=COC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 105, 105, 63, 105, 45, 14, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 162, 173, 173, 201, 201, 201, 201, 201, 162, 105, 63, 63, 14, 14, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 885 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918478 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918478 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918478/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918478 Building REAL300004918479 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918479' /scratch/stefan/7775246/working/building/REAL300004918479 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918479 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918479/0 /scratch/stefan/7775246/working/building/REAL300004918479 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/481 `/scratch/stefan/7775246/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1N=CC2=CC=CC=C2C1=O)C(=O)[O-]) `REAL300004918479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918479 none CC#CCC(NC(=O)CN1N=CC2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 90, 42, 42, 5, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 125, 125, 201, 201, 201, 201, 201, 90, 42, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 940 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918479 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918479 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918479/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918479 Building REAL300004918480 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918480' /scratch/stefan/7775246/working/building/REAL300004918480 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918480 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918480/0 /scratch/stefan/7775246/working/building/REAL300004918480 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/482 `/scratch/stefan/7775246/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(Cl)=C2)CCCC1)C(=O)[O-]) `REAL300004918480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918480 none CC#CCC(NC(=O)C1(C2=CC=CC(Cl)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 33, 11, 11, 1, 11, 1, 1, 9, 9, 8, 9, 9, 9, 1, 1, 1, 1, 33, 55, 55, 95, 95, 95, 95, 95, 33, 11, 9, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 16, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 480 number of broken/clashed sets: 189 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918480 none CC#CCC(NC(=O)C1(C2=CC=CC(Cl)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 88, 35, 35, 9, 35, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 88, 132, 132, 201, 201, 201, 201, 201, 88, 35, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1012 number of broken/clashed sets: 189 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918480 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918480 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918480/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918480 Building REAL300004918481 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918481' /scratch/stefan/7775246/working/building/REAL300004918481 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918481 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918481/0 /scratch/stefan/7775246/working/building/REAL300004918481 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/483 `/scratch/stefan/7775246/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(Cl)=C2)CC1)C(=O)[O-]) `REAL300004918481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918481 none CC#CCC(NC(=O)C1(C2=CC=CC(Cl)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 36, 13, 13, 1, 13, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 36, 61, 61, 98, 98, 98, 98, 98, 36, 13, 8, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 501 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918481 none CC#CCC(NC(=O)C1(C2=CC=CC(Cl)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 51, 51, 8, 51, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 102, 139, 139, 201, 201, 201, 201, 201, 102, 51, 1, 1, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 937 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918481 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918481 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918481/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918481 Building REAL300004918482 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918482' /scratch/stefan/7775246/working/building/REAL300004918482 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918482 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918482/0 /scratch/stefan/7775246/working/building/REAL300004918482 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/484 `/scratch/stefan/7775246/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=O)N(CC)C(=O)NC2=C1)C(=O)[O-]) `REAL300004918482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918482 none CC#CCC(NC(=O)C1=CC=C2C(=O)N(CC)C(=O)NC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 30, 41, 41, 67, 67, 67, 67, 67, 30, 7, 1, 1, 2, 2, 3, 3, 3, 1, 1] 127 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 7, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918482 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918482 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918482/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918482 Building REAL300004918483 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918483' /scratch/stefan/7775246/working/building/REAL300004918483 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918483 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918483/0 /scratch/stefan/7775246/working/building/REAL300004918483 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/485 `/scratch/stefan/7775246/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=C(Br)C=CC1=O)C(=O)[O-]) `REAL300004918483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918483 none CC#CCC(NC(=O)CN1C=C(Br)C=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 17, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 80, 37, 37, 5, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 125, 125, 201, 201, 201, 201, 201, 80, 37, 5, 5, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 1000 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918483 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918483 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918483/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918483 Building REAL300004918484 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918484' /scratch/stefan/7775246/working/building/REAL300004918484 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918484 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918484/0 /scratch/stefan/7775246/working/building/REAL300004918484 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/486 `/scratch/stefan/7775246/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CC1)C(=O)[O-]) `REAL300004918484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918484 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 37, 13, 13, 1, 13, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 37, 58, 58, 94, 94, 94, 94, 94, 37, 13, 8, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 449 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918484 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 50, 50, 8, 50, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 103, 138, 138, 201, 201, 201, 201, 201, 103, 50, 1, 1, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 939 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918484 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918484 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918484/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918484 Building REAL300004918485 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918485' /scratch/stefan/7775246/working/building/REAL300004918485 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918485 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918485/0 /scratch/stefan/7775246/working/building/REAL300004918485 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/487 `/scratch/stefan/7775246/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C(C)C)=C2)C(C)=C1)C(=O)[O-]) `REAL300004918485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918485 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C(C)C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 13, 13, 7, 1, 1, 1, 24, 36, 36, 50, 50, 50, 50, 50, 24, 9, 2, 2, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 51, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 313 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918485 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C(C)C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 89, 41, 41, 7, 41, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 7, 89, 132, 132, 164, 164, 164, 164, 164, 89, 41, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 845 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918485 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918485 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918485/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918485 Building REAL300004918486 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918486' /scratch/stefan/7775246/working/building/REAL300004918486 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918486 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918486/0 /scratch/stefan/7775246/working/building/REAL300004918486 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/488 `/scratch/stefan/7775246/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CS2)=N1)C(=O)[O-]) `REAL300004918486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918486 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 30, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 30, 48, 48, 77, 77, 77, 77, 77, 30, 11, 2, 2, 2, 13, 13, 13] 166 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 407 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918486 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 93, 48, 48, 13, 48, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 93, 128, 128, 166, 166, 166, 166, 166, 93, 48, 13, 13, 13, 1, 1, 1] 166 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 817 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918486 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918486 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918486/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918486 Building REAL300004918487 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918487' /scratch/stefan/7775246/working/building/REAL300004918487 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918487 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918487/0 /scratch/stefan/7775246/working/building/REAL300004918487 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/489 `/scratch/stefan/7775246/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C(C)(C)C)N=C1)C(=O)[O-]) `REAL300004918487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918487 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C(C)(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 36, 10, 10, 1, 10, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 1, 1, 36, 51, 51, 79, 79, 79, 79, 79, 36, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 84 rigid atoms, others: [6, 8, 9, 10, 14, 15, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918487 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918487 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918487/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918487 Building REAL300004918488 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918488' /scratch/stefan/7775246/working/building/REAL300004918488 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918488 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918488/0 /scratch/stefan/7775246/working/building/REAL300004918488 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/490 `/scratch/stefan/7775246/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC(=O)C1=CC=C(Br)S1)C(=O)[O-]) `REAL300004918488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918488 none CC#CCC(NC(=O)C(C)NC(=O)C1=CC=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 80, 80, 19, 80, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 130, 160, 160, 201, 201, 201, 201, 201, 130, 80, 19, 19, 19, 19, 7, 1, 1] 201 rigid atoms, others: [34, 35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 928 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918488 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918488 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918488/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918488 Building REAL300004918489 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918489' /scratch/stefan/7775246/working/building/REAL300004918489 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918489 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918489/0 /scratch/stefan/7775246/working/building/REAL300004918489 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/491 `/scratch/stefan/7775246/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C(C)(C)C)N=C1C)C(=O)[O-]) `REAL300004918489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918489 none CC#CCC(NC(=O)C1=C(C)N(C(C)(C)C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 47, 13, 13, 1, 13, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 47, 65, 65, 94, 94, 94, 94, 94, 47, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 94 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 462 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918489 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918489 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918489/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918489 Building REAL300004918490 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918490' /scratch/stefan/7775246/working/building/REAL300004918490 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918490 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918490/0 /scratch/stefan/7775246/working/building/REAL300004918490 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/492 `/scratch/stefan/7775246/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(OC(C)C)C=C2)=N1)C(=O)[O-]) `REAL300004918490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918490 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(OC(C)C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 4, 4, 2, 2, 20, 42, 42, 4, 4, 1, 14, 24, 24, 48, 48, 48, 48, 48, 14, 6, 1, 4, 4, 42, 42, 42, 42, 42, 42, 42, 4, 4] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 351 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918490 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(OC(C)C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 33, 13, 13, 4, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 10, 20, 20, 1, 1, 4, 33, 54, 54, 97, 97, 97, 97, 97, 33, 13, 4, 1, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1] 201 rigid atoms, others: [34, 35, 44, 11, 12, 13, 14, 15, 16, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 525 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918490 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918490 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918490/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918490 Building REAL300004918491 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918491' /scratch/stefan/7775246/working/building/REAL300004918491 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918491 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918491/0 /scratch/stefan/7775246/working/building/REAL300004918491 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/493 `/scratch/stefan/7775246/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C1=NC(C(C)(C)C)=NO1)C(=O)[O-]) `REAL300004918491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918491 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC(C(C)(C)C)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 35, 13, 13, 24, 39, 39, 71, 71, 71, 71, 71, 24, 9, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918491 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC(C(C)(C)C)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 90, 55, 55, 13, 55, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 90, 122, 122, 184, 184, 184, 184, 184, 90, 55, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 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: 889 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918491 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918491 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918491/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918491 Building REAL300004918492 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918492' /scratch/stefan/7775246/working/building/REAL300004918492 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918492 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918492/0 /scratch/stefan/7775246/working/building/REAL300004918492 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/494 `/scratch/stefan/7775246/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2CCOCC2)C=C1)C(=O)[O-]) `REAL300004918492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918492 none CC#CCC(NC(=O)C1=CC=C(OC2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 30, 1, 1, 9, 17, 17, 34, 34, 34, 34, 34, 9, 3, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [32, 43, 6, 8, 9, 10, 11, 12, 19, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 229 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918492 none CC#CCC(NC(=O)C1=CC=C(OC2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 54, 54, 14, 54, 6, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 30, 30, 119, 152, 152, 201, 201, 201, 201, 201, 119, 54, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43]) total number of confs: 980 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918492 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918492 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918492/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918492 Building REAL300004918493 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918493' /scratch/stefan/7775246/working/building/REAL300004918493 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918493 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918493/0 /scratch/stefan/7775246/working/building/REAL300004918493 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/495 `/scratch/stefan/7775246/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CS(=O)(=O)NC1CCC(C)CC1)C(=O)[O-]) `REAL300004918493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918493 none CC#CCC(NC(=O)CS(=O)(=O)NC1CCC(C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 146, 122, 122, 42, 122, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 146, 148, 148, 159, 159, 159, 159, 159, 146, 122, 42, 42, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 159 rigid atoms, others: [33, 34, 35, 36, 37, 38, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918493 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918493 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918493/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918493 Building REAL300004918494 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918494' /scratch/stefan/7775246/working/building/REAL300004918494 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918494 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918494/0 /scratch/stefan/7775246/working/building/REAL300004918494 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/496 `/scratch/stefan/7775246/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC(NC(=O)C2CCCC2)CC1)C(=O)[O-]) `REAL300004918494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918494 none CC#CCC(NC(=O)C1CCC(NC(=O)C2CCCC2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 1, 1, 27, 42, 42, 56, 56, 56, 56, 56, 27, 10, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 48, 49, 50, 51, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918494 none CC#CCC(NC(=O)C1CCC(NC(=O)C2CCCC2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 74, 74, 21, 74, 21, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 21, 21, 128, 155, 155, 201, 201, 201, 201, 201, 128, 74, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 897 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918494 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918494 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918494/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918494 Building REAL300004918495 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918495' /scratch/stefan/7775246/working/building/REAL300004918495 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918495 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918495/0 /scratch/stefan/7775246/working/building/REAL300004918495 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/497 `/scratch/stefan/7775246/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC(NC(=O)CC2CCCCC2)CC1)C(=O)[O-]) `REAL300004918495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918495 none CC#CCC(NC(=O)C1CCC(NC(=O)CC2CCCCC2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 31, 31, 31, 1, 1, 13, 23, 23, 37, 37, 37, 37, 37, 13, 6, 1, 1, 1, 1, 1, 1, 3, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 54, 57, 22, 23, 56, 55, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918495 none CC#CCC(NC(=O)C1CCC(NC(=O)CC2CCCCC2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 92, 92, 31, 92, 31, 31, 31, 18, 18, 5, 18, 1, 1, 1, 1, 1, 1, 1, 31, 31, 136, 167, 167, 201, 201, 201, 201, 201, 136, 92, 31, 31, 31, 31, 31, 31, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 201 rigid atoms, others: [48, 50, 51, 49, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 52, 47, 53] 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, 54, 55, 56, 57]) total number of confs: 984 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918495 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918495 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918495/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918495 Building REAL300004918496 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918496' /scratch/stefan/7775246/working/building/REAL300004918496 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918496 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918496/0 /scratch/stefan/7775246/working/building/REAL300004918496 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/498 `/scratch/stefan/7775246/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(OCCC)C=C2)=N1)C(=O)[O-]) `REAL300004918496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918496 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(OCCC)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 2, 3, 14, 18, 41, 3, 3, 1, 11, 13, 13, 26, 26, 26, 26, 26, 11, 4, 1, 4, 4, 18, 18, 41, 41, 41, 41, 41, 4, 4] 126 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918496 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(OCCC)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 27, 10, 10, 4, 10, 3, 3, 4, 1, 1, 1, 1, 1, 1, 5, 8, 19, 1, 1, 3, 27, 31, 31, 55, 55, 55, 55, 55, 27, 10, 3, 1, 1, 8, 8, 19, 19, 19, 19, 19, 1, 1] 126 rigid atoms, others: [34, 35, 44, 11, 12, 13, 14, 15, 16, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918496 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918496 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918496/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918496 Building REAL300004918497 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918497' /scratch/stefan/7775246/working/building/REAL300004918497 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918497 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918497/0 /scratch/stefan/7775246/working/building/REAL300004918497 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/499 `/scratch/stefan/7775246/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CCC)NC(=O)CC1=CC=CC=C1)C(=O)[O-]) `REAL300004918497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918497 none CC#CCC(NC(=O)C(CCC)NC(=O)CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 75, 50, 50, 15, 50, 8, 15, 42, 43, 8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 75, 76, 76, 108, 108, 108, 108, 108, 75, 50, 15, 42, 42, 43, 43, 43, 43, 43, 8, 4, 4, 1, 1, 1, 1, 1] 157 rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 47] 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: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918497 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918497 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918497/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918497 Building REAL300004918498 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918498' /scratch/stefan/7775246/working/building/REAL300004918498 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918498 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918498/0 /scratch/stefan/7775246/working/building/REAL300004918498 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/500 `/scratch/stefan/7775246/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2C=C(Br)C=N2)O1)C(=O)[O-]) `REAL300004918498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918498 none CC#CCC(NC(=O)C1=CC=C(CN2C=C(Br)C=N2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 26, 1, 18, 27, 27, 49, 49, 49, 49, 49, 18, 6, 1, 1, 9, 9, 26, 26] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918498 none CC#CCC(NC(=O)C1=CC=C(CN2C=C(Br)C=N2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 57, 57, 26, 57, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 26, 112, 148, 148, 201, 201, 201, 201, 201, 112, 57, 26, 26, 7, 7, 1, 1] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 971 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918498 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918498 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918498/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918498 Building REAL300004918499 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918499' /scratch/stefan/7775246/working/building/REAL300004918499 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918499 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918499/0 /scratch/stefan/7775246/working/building/REAL300004918499 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/501 `/scratch/stefan/7775246/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OCC(F)(F)F)C(OC)=C1)C(=O)[O-]) `REAL300004918499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918499 none CC#CCC(NC(=O)CCC1=CC=C(OCC(F)(F)F)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 10, 6, 6, 4, 6, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 24, 23, 1, 1, 3, 1, 10, 11, 11, 18, 18, 18, 18, 18, 10, 6, 4, 4, 2, 2, 1, 1, 23, 24, 3, 3, 3, 1] 85 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 45, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918499 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918499 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918499/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918499 Building REAL300004918500 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918500' /scratch/stefan/7775246/working/building/REAL300004918500 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918500 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918500/0 /scratch/stefan/7775246/working/building/REAL300004918500 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/502 `/scratch/stefan/7775246/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(NC(=O)NCCC)C=C1)C(=O)[O-]) `REAL300004918500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918500 none CC#CCC(NC(=O)CC1=CC=C(NC(=O)NCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 11, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 24, 1, 1, 11, 17, 17, 33, 33, 33, 33, 33, 11, 6, 3, 3, 1, 1, 6, 6, 18, 18, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 46, 45, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918500 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918500 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918500/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918500 Building REAL300004918501 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918501' /scratch/stefan/7775246/working/building/REAL300004918501 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918501 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918501/0 /scratch/stefan/7775246/working/building/REAL300004918501 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/503 `/scratch/stefan/7775246/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)CCC1CCCC1)C(=O)[O-]) `REAL300004918501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918501 none CC#CCC(NC(=O)CNC(=O)CCC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 142, 98, 98, 53, 98, 29, 29, 6, 29, 4, 1, 1, 1, 1, 1, 1, 142, 175, 175, 201, 201, 201, 201, 201, 142, 98, 53, 53, 29, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1050 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918501 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918501 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918501/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918501 Building REAL300004918502 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918502' /scratch/stefan/7775246/working/building/REAL300004918502 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918502 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918502/0 /scratch/stefan/7775246/working/building/REAL300004918502 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/504 `/scratch/stefan/7775246/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)N2CCCC2)C=C1)C(=O)[O-]) `REAL300004918502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918502 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 5, 3, 3, 2, 3, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 1, 1, 5, 7, 7, 17, 17, 17, 17, 17, 5, 3, 2, 2, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 31 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 48, 49, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918502 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 21, 18, 18, 13, 18, 13, 6, 6, 13, 13, 6, 1, 6, 6, 1, 1, 1, 1, 1, 13, 13, 21, 22, 22, 31, 31, 31, 31, 31, 21, 18, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 31 rigid atoms, others: [40, 41, 42, 43, 44, 45, 14, 47, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918502 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918502 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918502/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918502 Building REAL300004918503 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918503' /scratch/stefan/7775246/working/building/REAL300004918503 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918503 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918503/0 /scratch/stefan/7775246/working/building/REAL300004918503 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/505 `/scratch/stefan/7775246/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(OCC2=CC=CC=C2)C(OC)=C1)C(=O)[O-]) `REAL300004918503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918503 none CC#CCC(NC(=O)C1=CC(OC)=C(OCC2=CC=CC=C2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 13, 5, 5, 1, 5, 1, 1, 1, 1, 3, 1, 1, 2, 9, 23, 23, 10, 23, 23, 1, 1, 3, 1, 13, 20, 20, 35, 35, 35, 35, 35, 13, 5, 1, 3, 3, 3, 9, 9, 23, 23, 23, 23, 23, 4, 4, 4, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 13, 14, 50, 22, 23, 25] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918503 none CC#CCC(NC(=O)C1=CC(OC)=C(OCC2=CC=CC=C2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 103, 64, 64, 23, 64, 23, 23, 23, 23, 37, 13, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 36, 23, 103, 138, 138, 192, 192, 192, 192, 192, 103, 64, 23, 37, 37, 37, 3, 3, 1, 1, 1, 1, 1, 37, 37, 37, 23] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 1014 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918503 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918503 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918503/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918503 Building REAL300004918504 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918504' /scratch/stefan/7775246/working/building/REAL300004918504 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918504 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918504/0 /scratch/stefan/7775246/working/building/REAL300004918504 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/506 `/scratch/stefan/7775246/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(OCC(N)=O)C(OC)=C1)C(=O)[O-]) `REAL300004918504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918504 none CC#CCC(NC(=O)C1=CC(OC)=C(OCC(N)=O)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 11, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 13, 5, 5, 1, 5, 1, 1, 1, 1, 3, 1, 1, 2, 10, 38, 38, 1, 1, 3, 1, 13, 21, 21, 36, 36, 36, 36, 36, 13, 5, 1, 3, 3, 3, 10, 10, 38, 38, 3, 3, 3, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 44, 13, 14, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918504 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918504 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918504/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918504 Building REAL300004918505 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918505' /scratch/stefan/7775246/working/building/REAL300004918505 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918505 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918505/0 /scratch/stefan/7775246/working/building/REAL300004918505 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/507 `/scratch/stefan/7775246/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918505 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 50, 12, 12, 1, 12, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 50, 72, 72, 123, 123, 123, 123, 123, 50, 12, 4, 4, 3, 4, 4, 2, 2, 2, 1, 1, 1, 1] 127 rigid atoms, others: [6, 8, 9, 10, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 585 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918505 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 80, 28, 28, 4, 28, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 80, 101, 101, 127, 127, 127, 127, 127, 80, 28, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4] 127 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 608 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918505 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918505 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918505/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918505 Building REAL300004918506 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918506' /scratch/stefan/7775246/working/building/REAL300004918506 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918506 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918506/0 /scratch/stefan/7775246/working/building/REAL300004918506 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/508 `/scratch/stefan/7775246/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C(C)=N1)C(=O)[O-]) `REAL300004918506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918506 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 41, 12, 12, 1, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 41, 61, 61, 117, 117, 117, 117, 117, 41, 12, 5, 5, 5, 5, 2, 2, 2] 144 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 551 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918506 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 76, 31, 31, 5, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 76, 100, 100, 144, 144, 144, 144, 144, 76, 31, 1, 1, 1, 1, 5, 5, 5] 144 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 684 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918506 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918506 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918506/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918506 Building REAL300004918507 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918507' /scratch/stefan/7775246/working/building/REAL300004918507 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918507 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918507/0 /scratch/stefan/7775246/working/building/REAL300004918507 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/509 `/scratch/stefan/7775246/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1S(=O)(=O)CCC)C(=O)[O-]) `REAL300004918507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918507 none CC#CCC(NC(=O)C1CCCN1S(=O)(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 19, 26, 38, 38, 74, 74, 74, 74, 74, 26, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 19, 19, 19, 19, 19] 145 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 419 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918507 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918507 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918507/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918507 Building REAL300004918508 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918508' /scratch/stefan/7775246/working/building/REAL300004918508 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918508 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918508/0 /scratch/stefan/7775246/working/building/REAL300004918508 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/510 `/scratch/stefan/7775246/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)C2=CC=CC=C12)C(=O)[O-]) `REAL300004918508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918508 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 21, 8, 8, 1, 8, 1, 1, 1, 1, 8, 16, 16, 10, 16, 16, 1, 1, 1, 1, 1, 1, 21, 33, 33, 42, 42, 42, 42, 42, 21, 8, 1, 8, 8, 16, 16, 10, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [34, 43, 6, 8, 9, 10, 11, 44, 45, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918508 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 62, 62, 16, 62, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 122, 161, 161, 201, 201, 201, 201, 201, 122, 62, 16, 5, 5, 1, 1, 1, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 999 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918508 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918508 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918508/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918508 Building REAL300004918509 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918509' /scratch/stefan/7775246/working/building/REAL300004918509 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918509 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918509/0 /scratch/stefan/7775246/working/building/REAL300004918509 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/511 `/scratch/stefan/7775246/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(CCOC)C(=O)C=C1)C(=O)[O-]) `REAL300004918509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918509 none CC#CCC(NC(=O)C1=NN(CCOC)C(=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 27, 9, 9, 1, 9, 1, 1, 1, 1, 5, 12, 25, 1, 1, 1, 1, 27, 42, 42, 69, 69, 69, 69, 69, 27, 9, 5, 5, 12, 12, 25, 25, 25, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918509 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918509 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918509/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918509 Building REAL300004918510 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918510' /scratch/stefan/7775246/working/building/REAL300004918510 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918510 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918510/0 /scratch/stefan/7775246/working/building/REAL300004918510 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/512 `/scratch/stefan/7775246/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SCC(N)=O)C(=O)[O-]) `REAL300004918510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918510 none CC#CCC(NC(=O)C1=CC=CC=C1SCC(N)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 8, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 8, 32, 54, 54, 25, 36, 36, 69, 69, 69, 69, 69, 25, 10, 1, 1, 1, 1, 32, 32, 54, 54] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 478 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918510 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918510 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918510/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918510 Building REAL300004918511 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918511' /scratch/stefan/7775246/working/building/REAL300004918511 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918511 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918511/0 /scratch/stefan/7775246/working/building/REAL300004918511 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/513 `/scratch/stefan/7775246/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-]) `REAL300004918511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918511 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 37, 56, 56, 84, 84, 84, 84, 84, 37, 12, 1, 4, 4, 4, 4] 91 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918511 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 57, 29, 29, 4, 29, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 57, 67, 67, 91, 91, 91, 91, 91, 57, 29, 4, 1, 1, 1, 1] 91 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918511 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918511 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918511/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918511 Building REAL300004918512 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918512' /scratch/stefan/7775246/working/building/REAL300004918512 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918512 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918512/0 /scratch/stefan/7775246/working/building/REAL300004918512 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/514 `/scratch/stefan/7775246/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CSC(C)=N1)C(=O)[O-]) `REAL300004918512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918512 none CC#CCC(NC(=O)CSCC1=CSC(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 14, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 192, 162, 162, 81, 162, 28, 6, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 201, 201, 201, 201, 201, 192, 162, 80, 80, 6, 6, 1, 2, 2, 2] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918512 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918512 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918512/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918512 Building REAL300004918513 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918513' /scratch/stefan/7775246/working/building/REAL300004918513 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918513 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918513/0 /scratch/stefan/7775246/working/building/REAL300004918513 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/515 `/scratch/stefan/7775246/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCC(N)=O)C(OC)=C1)C(=O)[O-]) `REAL300004918513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918513 none CC#CCC(NC(=O)C=CC1=CC=C(OCC(N)=O)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 11, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 29, 25, 25, 5, 25, 5, 1, 1, 1, 1, 1, 1, 9, 33, 56, 56, 1, 1, 3, 1, 29, 29, 29, 36, 36, 36, 36, 36, 29, 25, 5, 5, 1, 1, 33, 33, 56, 56, 3, 3, 3, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918513 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918513 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918513/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918513 Building REAL300004918514 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918514' /scratch/stefan/7775246/working/building/REAL300004918514 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918514 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918514/0 /scratch/stefan/7775246/working/building/REAL300004918514 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/516 `/scratch/stefan/7775246/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1N=NC2=CC=CC=C2C1=O)C(=O)[O-]) `REAL300004918514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918514 none CC#CCC(NC(=O)CN1N=NC2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 96, 46, 46, 5, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 134, 134, 201, 201, 201, 201, 201, 96, 46, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 962 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918514 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918514 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918514/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918514 Building REAL300004918515 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918515' /scratch/stefan/7775246/working/building/REAL300004918515 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918515 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918515/0 /scratch/stefan/7775246/working/building/REAL300004918515 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/517 `/scratch/stefan/7775246/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004918515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918515 none CC#CCC(NC(=O)CCC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 73, 73, 16, 73, 8, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 126, 170, 170, 201, 201, 201, 201, 201, 126, 73, 16, 16, 8, 8, 1, 4, 4, 2, 4, 4, 1] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 1072 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918515 none CC#CCC(NC(=O)CCC1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 137, 90, 90, 28, 90, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 141, 173, 173, 201, 201, 201, 201, 201, 141, 90, 28, 28, 19, 19, 4, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41]) total number of confs: 990 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918515 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918515 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918515/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918515 Building REAL300004918516 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918516' /scratch/stefan/7775246/working/building/REAL300004918516 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918516 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918516/0 /scratch/stefan/7775246/working/building/REAL300004918516 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/518 `/scratch/stefan/7775246/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(C)N2N=C(C(F)(F)F)N=C2N=C1C)C(=O)[O-]) `REAL300004918516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918516 none CC#CCC(NC(=O)CCC1=C(C)N2N=C(C(F)(F)F)N=C2N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 8, 8, 1, 5, 15, 15, 15, 8, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 54, 19, 19, 3, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 54, 61, 61, 68, 68, 68, 68, 68, 54, 19, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 68 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 326 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918516 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918516 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918516/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918516 Building REAL300004918517 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918517' /scratch/stefan/7775246/working/building/REAL300004918517 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918517 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918517/0 /scratch/stefan/7775246/working/building/REAL300004918517 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/519 `/scratch/stefan/7775246/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(Br)S1)C(=O)[O-]) `REAL300004918517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918517 none CC#CCC(NC(=O)CCCC1=CC=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 66, 66, 18, 66, 11, 7, 1, 1, 1, 1, 1, 1, 1, 109, 148, 148, 201, 201, 201, 201, 201, 109, 66, 18, 18, 11, 11, 7, 7, 1, 1] 201 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1012 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918517 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918517 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918517/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918517 Building REAL300004918518 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918518' /scratch/stefan/7775246/working/building/REAL300004918518 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918518 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918518/0 /scratch/stefan/7775246/working/building/REAL300004918518 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/520 `/scratch/stefan/7775246/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=NN=C(C3=CC=C(C)C=C3)O2)C=C1)C(=O)[O-]) `REAL300004918518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918518 none CC#CCC(NC(=O)C1=CC=C(C2=NN=C(C3=CC=C(C)C=C3)O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 8, 8, 10, 10, 4, 1, 1, 15, 23, 23, 45, 45, 45, 45, 45, 15, 4, 1, 1, 10, 10, 11, 11, 11, 10, 11, 1, 1] 80 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918518 none CC#CCC(NC(=O)C1=CC=C(C2=NN=C(C3=CC=C(C)C=C3)O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 56, 24, 24, 11, 24, 11, 10, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 56, 67, 67, 80, 80, 80, 80, 80, 56, 24, 10, 10, 1, 1, 2, 2, 2, 1, 1, 11, 11] 80 rigid atoms, others: [38, 39, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46]) total number of confs: 366 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918518 none CC#CCC(NC(=O)C1=CC=C(C2=NN=C(C3=CC=C(C)C=C3)O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 38, 13, 13, 4, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 1, 4, 4, 38, 52, 52, 80, 80, 80, 80, 80, 38, 13, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4] 80 rigid atoms, others: [11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918518 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918518 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918518/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918518 Building REAL300004918519 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918519' /scratch/stefan/7775246/working/building/REAL300004918519 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918519 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918519/0 /scratch/stefan/7775246/working/building/REAL300004918519 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/521 `/scratch/stefan/7775246/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)N1N=NC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-]) `REAL300004918519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918519 none CC#CCC(NC(=O)C(CC)N1N=NC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 77, 48, 48, 11, 48, 1, 11, 18, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 77, 81, 81, 106, 106, 106, 106, 106, 77, 48, 11, 18, 18, 18, 18, 18, 4, 4, 4, 4] 110 rigid atoms, others: [8, 11, 12, 13, 14, 15, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918519 none CC#CCC(NC(=O)C(CC)N1N=NC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 89, 69, 69, 23, 69, 4, 23, 34, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 89, 91, 91, 109, 109, 109, 109, 109, 89, 69, 23, 34, 34, 34, 34, 34, 1, 1, 1, 1] 110 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918519 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918519 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918519/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918519 Building REAL300004918520 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918520' /scratch/stefan/7775246/working/building/REAL300004918520 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918520 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918520/0 /scratch/stefan/7775246/working/building/REAL300004918520 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/522 `/scratch/stefan/7775246/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=CC=C1F)C(=O)[O-]) `REAL300004918520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918520 none CC#CCC(NC(=O)CCSC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 170, 135, 135, 35, 135, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 201, 201, 201, 201, 170, 135, 34, 34, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 889 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918520 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918520 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918520/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918520 Building REAL300004918521 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918521' /scratch/stefan/7775246/working/building/REAL300004918521 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918521 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918521/0 /scratch/stefan/7775246/working/building/REAL300004918521 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/523 `/scratch/stefan/7775246/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCN1C(=O)N(CCC)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918521 none CC#CCC(NC(=O)CCN1C(=O)N(CCC)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 47, 24, 24, 7, 24, 4, 1, 1, 1, 1, 1, 1, 3, 7, 1, 1, 1, 1, 1, 1, 47, 70, 70, 95, 95, 95, 95, 95, 47, 24, 7, 7, 4, 4, 3, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [45, 9, 10, 11, 12, 13, 14, 44, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918521 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918521 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918521/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918521 Building REAL300004918522 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918522' /scratch/stefan/7775246/working/building/REAL300004918522 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918522 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918522/0 /scratch/stefan/7775246/working/building/REAL300004918522 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/524 `/scratch/stefan/7775246/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(Cl)=CC=C2OC1)C(=O)[O-]) `REAL300004918522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918522 none CC#CCC(NC(=O)C1=CC2=CC(Cl)=CC=C2OC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 55, 55, 88, 88, 88, 88, 88, 38, 12, 1, 1, 1, 1, 1, 1] 88 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918522 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918522 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918522/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918522 Building REAL300004918523 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918523' /scratch/stefan/7775246/working/building/REAL300004918523 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918523 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918523/0 /scratch/stefan/7775246/working/building/REAL300004918523 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/525 `/scratch/stefan/7775246/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C2CC2C)O1)C(=O)[O-]) `REAL300004918523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918523 none CC#CCC(NC(=O)C=CC1=CC=C(C2CC2C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 57, 35, 35, 9, 35, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 57, 76, 76, 112, 112, 112, 112, 112, 57, 35, 9, 9, 1, 1, 9, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918523 none CC#CCC(NC(=O)C=CC1=CC=C(C2CC2C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 87, 87, 33, 87, 33, 10, 9, 9, 10, 1, 1, 1, 1, 1, 10, 128, 147, 147, 201, 201, 201, 201, 201, 128, 87, 33, 33, 10, 10, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 867 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918523 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918523 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918523/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918523 Building REAL300004918524 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918524' /scratch/stefan/7775246/working/building/REAL300004918524 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918524 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918524/0 /scratch/stefan/7775246/working/building/REAL300004918524 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/526 `/scratch/stefan/7775246/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(N2CCCC2=O)=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918524 none CC#CCC(NC(=O)C1=CC(N2CCCC2=O)=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 24, 7, 7, 1, 7, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 2, 1, 24, 39, 39, 81, 81, 81, 81, 81, 24, 7, 1, 8, 8, 8, 8, 8, 8, 1, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 17, 18, 19, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918524 none CC#CCC(NC(=O)C1=CC(N2CCCC2=O)=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 31, 31, 8, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 95, 135, 135, 201, 201, 201, 201, 201, 95, 31, 8, 1, 1, 1, 1, 1, 1, 8, 8] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 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, 41, 42]) total number of confs: 997 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918524 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918524 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918524/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918524 Building REAL300004918525 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918525' /scratch/stefan/7775246/working/building/REAL300004918525 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918525 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918525/0 /scratch/stefan/7775246/working/building/REAL300004918525 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/527 `/scratch/stefan/7775246/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC(=O)N(CCC)CCC)C(=O)[O-]) `REAL300004918525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918525 none CC#CCC(NC(=O)CCCC(=O)N(CCC)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 23 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918525 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918525 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918525/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918525 Building REAL300004918526 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918526' /scratch/stefan/7775246/working/building/REAL300004918526 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918526 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918526/0 /scratch/stefan/7775246/working/building/REAL300004918526 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/528 `/scratch/stefan/7775246/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)N(CCC)CCC)C(=O)[O-]) `REAL300004918526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918526 none CC#CCC(NC(=O)CCC(=O)N(CCC)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 5, 5, 3, 5, 1, 1, 1, 7, 7, 11, 17, 17, 11, 16, 17, 7, 9, 9, 11, 11, 11, 11, 11, 7, 5, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 17, 16, 16, 17, 17, 17, 17, 17] 31 rigid atoms, others: [8, 9, 10, 32, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 8 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918526 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918526 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918526/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918526 Building REAL300004918527 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918527' /scratch/stefan/7775246/working/building/REAL300004918527 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918527 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918527/0 /scratch/stefan/7775246/working/building/REAL300004918527 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/529 `/scratch/stefan/7775246/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=NNC=N2)S1)C(=O)[O-]) `REAL300004918527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918527 none CC#CCC(NC(=O)C1=C(C)N=C(C2=NNC=N2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 36, 55, 55, 87, 87, 87, 87, 87, 36, 11, 2, 2, 2, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 436 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918527 none CC#CCC(NC(=O)C1=C(C)N=C(C2=NNC=N2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 78, 78, 13, 77, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 138, 161, 161, 201, 201, 201, 201, 201, 138, 78, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 866 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918527 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918527 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918527/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918527 Building REAL300004918528 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918528' /scratch/stefan/7775246/working/building/REAL300004918528 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918528 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918528/0 /scratch/stefan/7775246/working/building/REAL300004918528 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/530 `/scratch/stefan/7775246/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2Cl)N=N1)C(=O)[O-]) `REAL300004918528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918528 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2Cl)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 35, 50, 50, 70, 70, 70, 70, 70, 35, 10, 2, 2, 2, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 374 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918528 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2Cl)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 47, 47, 7, 47, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 119, 153, 153, 201, 201, 201, 201, 201, 119, 47, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 962 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918528 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918528 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918528/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918528 Building REAL300004918529 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918529' /scratch/stefan/7775246/working/building/REAL300004918529 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918529 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918529/0 /scratch/stefan/7775246/working/building/REAL300004918529 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/531 `/scratch/stefan/7775246/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C(N)=O)=C1)C(=O)[O-]) `REAL300004918529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918529 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C(N)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 27, 9, 10, 1, 10, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 4, 4, 1, 27, 42, 42, 76, 76, 76, 76, 76, 27, 10, 5, 5, 2, 5, 5, 4, 4, 1] 143 rigid atoms, others: [6, 39, 8, 9, 10, 11, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918529 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C(N)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 61, 24, 24, 5, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 5, 61, 89, 89, 129, 129, 129, 129, 129, 61, 24, 1, 1, 1, 1, 1, 8, 8, 5] 143 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918529 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918529 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918529/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918529 Building REAL300004918530 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918530' /scratch/stefan/7775246/working/building/REAL300004918530 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918530 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918530/0 /scratch/stefan/7775246/working/building/REAL300004918530 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/532 `/scratch/stefan/7775246/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=CC=C1OC)C(=O)[O-]) `REAL300004918530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918530 none CC#CCC(NC(=O)CC(C)C1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 90, 49, 49, 14, 49, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 90, 123, 123, 170, 170, 170, 170, 170, 90, 49, 14, 14, 4, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 843 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918530 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918530 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918530/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918530 Building REAL300004918531 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918531' /scratch/stefan/7775246/working/building/REAL300004918531 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918531 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918531/0 /scratch/stefan/7775246/working/building/REAL300004918531 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/533 `/scratch/stefan/7775246/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(NC(C)=O)C1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004918531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918531 none CC#CCC(NC(=O)CC(NC(C)=O)C1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [92, 92, 92, 64, 38, 38, 12, 38, 5, 1, 5, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 19, 64, 76, 76, 92, 92, 92, 92, 92, 64, 38, 12, 12, 5, 7, 7, 7, 7, 1, 1, 1, 1, 19, 19, 19, 19, 19] 123 rigid atoms, others: [40, 9, 42, 43, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 510 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918531 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918531 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918531/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918531 Building REAL300004918532 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918532' /scratch/stefan/7775246/working/building/REAL300004918532 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918532 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918532/0 /scratch/stefan/7775246/working/building/REAL300004918532 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/534 `/scratch/stefan/7775246/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(SC)=C(OC)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918532 none CC#CCC(NC(=O)C1=CC(SC)=C(OC)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 5, 1, 12, 5, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 17, 6, 6, 1, 6, 1, 1, 1, 1, 10, 1, 1, 4, 1, 1, 1, 2, 2, 17, 29, 29, 67, 67, 67, 67, 67, 17, 6, 1, 10, 10, 10, 4, 4, 4, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 13, 14, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918532 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918532 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918532/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918532 Building REAL300004918533 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918533' /scratch/stefan/7775246/working/building/REAL300004918533 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918533 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918533/0 /scratch/stefan/7775246/working/building/REAL300004918533 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/535 `/scratch/stefan/7775246/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004918533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918533 none CC#CCC(NC(=O)C(C)CC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 51, 51, 10, 51, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 143, 143, 201, 201, 201, 201, 201, 109, 51, 10, 10, 10, 10, 5, 5, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 969 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918533 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918533 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918533/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918533 Building REAL300004918534 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918534' /scratch/stefan/7775246/working/building/REAL300004918534 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918534 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918534/0 /scratch/stefan/7775246/working/building/REAL300004918534 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/536 `/scratch/stefan/7775246/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OCC)C(=O)[O-]) `REAL300004918534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918534 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 33, 11, 11, 1, 11, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 10, 41, 33, 54, 54, 94, 94, 94, 94, 94, 33, 11, 4, 4, 2, 4, 4, 1, 41, 41, 42, 42, 42] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918534 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 43, 18, 18, 4, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 52, 43, 67, 67, 106, 106, 106, 106, 106, 43, 18, 1, 1, 1, 1, 1, 4, 52, 52, 52, 52, 52] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918534 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918534 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918534/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918534 Building REAL300004918535 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918535' /scratch/stefan/7775246/working/building/REAL300004918535 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918535 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918535/0 /scratch/stefan/7775246/working/building/REAL300004918535 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/537 `/scratch/stefan/7775246/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C1=CC=CC=C1)C(F)(F)F)C(=O)[O-]) `REAL300004918535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918535 none CC#CCC(NC(=O)CC(C1=CC=CC=C1)C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1] 3 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918535 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918535 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918535/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918535 Building REAL300004918536 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918536' /scratch/stefan/7775246/working/building/REAL300004918536 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918536 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918536/0 /scratch/stefan/7775246/working/building/REAL300004918536 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/538 `/scratch/stefan/7775246/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=C3OCOC3=C2)S1)C(=O)[O-]) `REAL300004918536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918536 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C3OCOC3=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 45, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 4, 1, 45, 70, 70, 98, 98, 98, 98, 98, 45, 13, 1, 5, 5, 5, 5, 5] 148 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918536 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C3OCOC3=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 90, 37, 37, 4, 37, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 90, 108, 108, 148, 148, 148, 148, 148, 90, 37, 5, 1, 1, 1, 1, 1] 148 rigid atoms, others: [33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 656 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918536 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918536 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918536/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918536 Building REAL300004918537 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918537' /scratch/stefan/7775246/working/building/REAL300004918537 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918537 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918537/0 /scratch/stefan/7775246/working/building/REAL300004918537 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/539 `/scratch/stefan/7775246/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1CC2=CC=CC=C2C1=O)C(=O)[O-]) `REAL300004918537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918537 none CC#CCC(NC(=O)CN1CC2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 58, 57, 7, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 150, 150, 201, 201, 201, 201, 201, 109, 57, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 989 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918537 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918537 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918537/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918537 Building REAL300004918538 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918538' /scratch/stefan/7775246/working/building/REAL300004918538 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918538 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918538/0 /scratch/stefan/7775246/working/building/REAL300004918538 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/540 `/scratch/stefan/7775246/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1OCCC2=C1SC=C2)C(=O)[O-]) `REAL300004918538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918538 none CC#CCC(NC(=O)CC1OCCC2=C1SC=C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 48, 48, 8, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 141, 141, 201, 201, 201, 201, 201, 109, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 959 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918538 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918538 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918538/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918538 Building REAL300004918539 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918539' /scratch/stefan/7775246/working/building/REAL300004918539 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918539 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918539/0 /scratch/stefan/7775246/working/building/REAL300004918539 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/541 `/scratch/stefan/7775246/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1OCCC2=CC=CC=C21)C(=O)[O-]) `REAL300004918539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918539 none CC#CCC(NC(=O)CC1OCCC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 47, 47, 8, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 155, 155, 201, 201, 201, 201, 201, 110, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1017 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918539 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918539 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918539/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918539 Building REAL300004918540 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918540' /scratch/stefan/7775246/working/building/REAL300004918540 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918540 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918540/0 /scratch/stefan/7775246/working/building/REAL300004918540 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/542 `/scratch/stefan/7775246/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918540 none CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 20, 20, 20, 20, 20, 1, 14, 21, 21, 37, 37, 37, 37, 37, 14, 5, 1, 1, 1, 19, 19, 19, 20, 20, 20, 20, 20, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 45, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918540 none CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 56, 56, 20, 56, 20, 20, 20, 20, 10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 20, 114, 148, 148, 201, 201, 201, 201, 201, 114, 56, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 20] 201 rigid atoms, others: [40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 988 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918540 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918540 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918540/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918540 Building REAL300004918541 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918541' /scratch/stefan/7775246/working/building/REAL300004918541 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918541 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918541/0 /scratch/stefan/7775246/working/building/REAL300004918541 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/543 `/scratch/stefan/7775246/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N(CC)CC)=C1)C(=O)[O-]) `REAL300004918541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918541 none CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N(CC)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 3, 9, 1, 18, 28, 28, 69, 69, 69, 69, 69, 18, 6, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 48, 22] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 356 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918541 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918541 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918541/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918541 Building REAL300004918542 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918542' /scratch/stefan/7775246/working/building/REAL300004918542 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918542 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918542/0 /scratch/stefan/7775246/working/building/REAL300004918542 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/544 `/scratch/stefan/7775246/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918542 none CC#CCC(NC(=O)C(C)SC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 66, 66, 17, 66, 6, 17, 1, 1, 1, 1, 1, 1, 1, 1, 118, 150, 150, 201, 201, 201, 201, 201, 118, 66, 17, 17, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 969 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918542 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918542 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918542/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918542 Building REAL300004918543 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918543' /scratch/stefan/7775246/working/building/REAL300004918543 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918543 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918543/0 /scratch/stefan/7775246/working/building/REAL300004918543 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/545 `/scratch/stefan/7775246/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(C)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-]) `REAL300004918543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918543 none CC#CCC(NC(=O)C=CC1=C(C)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 48, 25, 25, 7, 25, 7, 1, 1, 1, 1, 1, 1, 5, 13, 13, 10, 13, 13, 13, 1, 1, 1, 48, 49, 49, 59, 59, 59, 59, 59, 48, 25, 7, 7, 2, 2, 2, 5, 5, 13, 13, 12, 13, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918543 none CC#CCC(NC(=O)C=CC1=C(C)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 120, 120, 61, 120, 61, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 179, 179, 179, 201, 201, 201, 201, 201, 179, 120, 61, 61, 13, 13, 13, 6, 6, 1, 1, 1, 1, 13, 13, 13] 201 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48]) total number of confs: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918543 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918543 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918543/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918543 Building REAL300004918544 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918544' /scratch/stefan/7775246/working/building/REAL300004918544 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918544 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918544/0 /scratch/stefan/7775246/working/building/REAL300004918544 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/546 `/scratch/stefan/7775246/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(Cl)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-]) `REAL300004918544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918544 none CC#CCC(NC(=O)C=CC1=C(Cl)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 79, 38, 38, 7, 38, 7, 1, 1, 1, 1, 1, 1, 5, 9, 9, 7, 9, 9, 9, 1, 1, 1, 79, 80, 80, 100, 100, 100, 100, 100, 79, 38, 7, 7, 5, 5, 9, 9, 10, 10, 10, 9, 9, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918544 none CC#CCC(NC(=O)C=CC1=C(Cl)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 193, 128, 128, 40, 128, 40, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 193, 193, 193, 201, 201, 201, 201, 201, 193, 128, 40, 40, 3, 3, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10] 201 rigid atoms, others: [39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47, 48]) total number of confs: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918544 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918544 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918544/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918544 Building REAL300004918545 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918545' /scratch/stefan/7775246/working/building/REAL300004918545 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918545 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918545/0 /scratch/stefan/7775246/working/building/REAL300004918545 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/547 `/scratch/stefan/7775246/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=C(C)C(C)=C1)C(=O)[O-]) `REAL300004918545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918545 none CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=C(C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 7, 13, 28, 28, 28, 22, 32, 32, 48, 48, 48, 48, 48, 22, 9, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918545 none CC#CCC(NC(=O)C1=CC=CC=C1C(=O)C1=CC=C(C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 87, 87, 28, 87, 28, 28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 131, 163, 163, 201, 201, 201, 201, 201, 131, 87, 28, 28, 28, 28, 1, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [38, 39, 46, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 939 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918545 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918545 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918545/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918545 Building REAL300004918546 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918546' /scratch/stefan/7775246/working/building/REAL300004918546 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918546 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918546/0 /scratch/stefan/7775246/working/building/REAL300004918546 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/548 `/scratch/stefan/7775246/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)NC2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004918546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918546 none CC#CCC(NC(=O)C1CCN(C(=O)NC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 1, 1, 20, 32, 32, 51, 51, 51, 51, 51, 20, 8, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 45, 46, 44, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43]) total number of confs: 276 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918546 none CC#CCC(NC(=O)C1CCN(C(=O)NC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 66, 66, 14, 66, 14, 14, 14, 5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 117, 159, 159, 201, 201, 201, 201, 201, 117, 66, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47]) total number of confs: 1012 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918546 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918546 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918546/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918546 Building REAL300004918547 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918547' /scratch/stefan/7775246/working/building/REAL300004918547 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004918547 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918547/0 /scratch/stefan/7775246/working/building/REAL300004918547 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/549 `/scratch/stefan/7775246/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918547 none CC#CCC(NC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 9, 17, 17, 28, 28, 28, 28, 28, 9, 3, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918547 none CC#CCC(NC(=O)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 33, 33, 9, 33, 5, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 17, 17, 104, 141, 141, 201, 201, 201, 201, 201, 104, 33, 17, 17, 5, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 1021 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918547 /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `1' /scratch/stefan/7775246/working/building/REAL300004918547/1 /scratch/stefan/7775246/working/building/REAL300004918547 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/550 `/scratch/stefan/7775246/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918547.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004918547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918547 none CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 9, 16, 16, 30, 30, 30, 30, 30, 9, 3, 1, 1, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918547 none CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 98, 34, 34, 9, 34, 5, 18, 18, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 98, 137, 137, 201, 201, 201, 201, 201, 98, 34, 18, 18, 1, 1, 1, 1, 1, 18, 18] 201 rigid atoms, others: [36, 37, 38, 39, 40, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 1020 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918547 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918547 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918547/0.* 1: /scratch/stefan/7775246/working/building/REAL300004918547/1.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918547 Building REAL300004918548 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918548' /scratch/stefan/7775246/working/building/REAL300004918548 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004918548 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918548/0 /scratch/stefan/7775246/working/building/REAL300004918548 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/551 `/scratch/stefan/7775246/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918548 none CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 1, 14, 20, 20, 31, 31, 31, 31, 31, 14, 5, 1, 1, 1, 7, 19, 19, 19, 19, 19, 1] 119 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 43, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918548 none CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 70, 31, 31, 19, 31, 19, 19, 19, 19, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 19, 70, 94, 94, 119, 119, 119, 119, 119, 70, 31, 19, 19, 19, 5, 1, 1, 1, 1, 1, 19] 119 rigid atoms, others: [38, 39, 40, 41, 42, 14, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918548 /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `1' /scratch/stefan/7775246/working/building/REAL300004918548/1 /scratch/stefan/7775246/working/building/REAL300004918548 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/552 `/scratch/stefan/7775246/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC([N-]S(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918548.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004918548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918548 none CC#CCC(NC(=O)C1=CC=CC([N-]S(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 1, 15, 20, 20, 40, 40, 40, 40, 40, 15, 5, 1, 1, 1, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918548 none CC#CCC(NC(=O)C1=CC=CC([N-]S(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 111, 50, 50, 15, 50, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 111, 143, 143, 201, 201, 201, 201, 201, 111, 50, 15, 15, 15, 1, 1, 1, 1, 1, 15] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 976 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918548 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918548 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918548/0.* 1: /scratch/stefan/7775246/working/building/REAL300004918548/1.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918548 Building REAL300004918549 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918549' /scratch/stefan/7775246/working/building/REAL300004918549 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918549 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918549/0 /scratch/stefan/7775246/working/building/REAL300004918549 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/553 `/scratch/stefan/7775246/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(C)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-]) `REAL300004918549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918549 none CC#CCC(NC(=O)C=CC1=C(C)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 87, 44, 44, 7, 44, 7, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 1, 1, 1, 87, 87, 87, 108, 108, 108, 108, 108, 87, 44, 7, 7, 2, 2, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 461 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918549 none CC#CCC(NC(=O)C=CC1=C(C)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 191, 125, 125, 42, 125, 42, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 191, 191, 191, 201, 201, 201, 201, 201, 191, 125, 42, 42, 11, 11, 11, 4, 4, 1, 1, 2, 2, 2, 1, 1, 11, 11, 11] 201 rigid atoms, others: [48, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 49, 50, 51]) total number of confs: 742 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918549 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918549 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918549/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918549 Building REAL300004918550 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918550' /scratch/stefan/7775246/working/building/REAL300004918550 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918550 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918550/0 /scratch/stefan/7775246/working/building/REAL300004918550 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/554 `/scratch/stefan/7775246/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC(=O)NC12CC3CC(CC(C3)C1)C2)C(=O)[O-]) `REAL300004918550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918550 none CC#CCC(NC(=O)CCNC(=O)NC12CC3CC(CC(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 74, 52, 52, 17, 52, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 84, 84, 84, 84, 84, 75, 52, 17, 17, 10, 10, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918550 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918550 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918550/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918550 Building REAL300004918551 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918551' /scratch/stefan/7775246/working/building/REAL300004918551 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918551 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918551/0 /scratch/stefan/7775246/working/building/REAL300004918551 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/555 `/scratch/stefan/7775246/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Br)=CC=C1OC)C(=O)[O-]) `REAL300004918551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918551 none CC#CCC(NC(=O)C=CC1=CC(Br)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 89, 51, 49, 9, 52, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 89, 130, 130, 180, 180, 180, 180, 180, 89, 52, 9, 9, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 892 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918551 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918551 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918551/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918551 Building REAL300004918552 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918552' /scratch/stefan/7775246/working/building/REAL300004918552 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918552 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918552/0 /scratch/stefan/7775246/working/building/REAL300004918552 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/556 `/scratch/stefan/7775246/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918552 none CC#CCC(NC(=O)C=CC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 47, 18, 18, 4, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 47, 60, 60, 79, 79, 79, 79, 79, 47, 19, 4, 4, 1, 1, 1, 1] 79 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 378 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918552 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918552 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918552/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918552 Building REAL300004918553 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918553' /scratch/stefan/7775246/working/building/REAL300004918553 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918553 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918553/0 /scratch/stefan/7775246/working/building/REAL300004918553 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/557 `/scratch/stefan/7775246/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918553 none CC#CCC(NC(=O)CCSC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 89, 89, 21, 89, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 128, 174, 174, 201, 201, 201, 201, 201, 128, 89, 21, 21, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 993 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918553 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918553 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918553/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918553 Building REAL300004918554 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918554' /scratch/stefan/7775246/working/building/REAL300004918554 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918554 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918554/0 /scratch/stefan/7775246/working/building/REAL300004918554 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/558 `/scratch/stefan/7775246/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918554 none CC#CCC(NC(=O)CSC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 72, 72, 24, 72, 6, 1, 1, 1, 1, 1, 1, 1, 1, 116, 153, 153, 201, 201, 201, 201, 201, 116, 72, 24, 24, 1, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 1004 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918554 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918554 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918554/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918554 Building REAL300004918555 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918555' /scratch/stefan/7775246/working/building/REAL300004918555 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918555 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918555/0 /scratch/stefan/7775246/working/building/REAL300004918555 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/559 `/scratch/stefan/7775246/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918555 none CC#CCC(NC(=O)C=CC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 55, 21, 21, 4, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 55, 68, 68, 86, 86, 86, 86, 86, 55, 22, 4, 4, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 398 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918555 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918555 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918555/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918555 Building REAL300004918556 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918556' /scratch/stefan/7775246/working/building/REAL300004918556 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918556 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918556/0 /scratch/stefan/7775246/working/building/REAL300004918556 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/560 `/scratch/stefan/7775246/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-]) `REAL300004918556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918556 none CC#CCC(NC(=O)C1=C(Cl)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 5, 12, 12, 7, 12, 12, 12, 1, 1, 1, 20, 34, 34, 48, 48, 48, 48, 48, 20, 6, 5, 5, 12, 12, 13, 13, 13, 12, 12, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918556 none CC#CCC(NC(=O)C1=C(Cl)N(CC2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 56, 56, 12, 56, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 123, 153, 153, 201, 201, 201, 201, 201, 123, 56, 4, 4, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13] 201 rigid atoms, others: [35, 36, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43, 44]) total number of confs: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918556 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918556 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918556/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918556 Building REAL300004918557 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918557' /scratch/stefan/7775246/working/building/REAL300004918557 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918557 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918557/0 /scratch/stefan/7775246/working/building/REAL300004918557 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/561 `/scratch/stefan/7775246/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CCSC)NC(=O)C1=CC=CO1)C(=O)[O-]) `REAL300004918557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918557 none CC#CCC(NC(=O)C(CCSC)NC(=O)C1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 62, 32, 32, 15, 32, 6, 15, 43, 45, 91, 6, 1, 6, 1, 1, 1, 1, 1, 62, 83, 83, 107, 107, 107, 107, 107, 62, 32, 15, 45, 45, 45, 45, 91, 91, 91, 6, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 756 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918557 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918557 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918557/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918557 Building REAL300004918558 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918558' /scratch/stefan/7775246/working/building/REAL300004918558 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918558 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918558/0 /scratch/stefan/7775246/working/building/REAL300004918558 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/562 `/scratch/stefan/7775246/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=O)N(C3CCCCC3)C(=O)C2=C1)C(=O)[O-]) `REAL300004918558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918558 none CC#CCC(NC(=O)C1=CC=C2C(=O)N(C3CCCCC3)C(=O)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 10, 10, 1, 1, 1, 1, 30, 44, 44, 80, 80, 80, 80, 80, 30, 7, 1, 1, 10, 11, 11, 10, 11, 11, 11, 10, 11, 11, 11, 1] 187 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 48, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918558 none CC#CCC(NC(=O)C1=CC=C2C(=O)N(C3CCCCC3)C(=O)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 101, 44, 44, 11, 44, 10, 10, 10, 10, 10, 11, 1, 1, 1, 1, 1, 1, 1, 10, 11, 10, 10, 101, 131, 131, 187, 187, 187, 187, 187, 101, 44, 10, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 187 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 47] 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, 48]) total number of confs: 866 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918558 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918558 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918558/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918558 Building REAL300004918559 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918559' /scratch/stefan/7775246/working/building/REAL300004918559 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918559 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918559/0 /scratch/stefan/7775246/working/building/REAL300004918559 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/563 `/scratch/stefan/7775246/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC(=O)CC1=CC=CC=C1)C(=O)[O-]) `REAL300004918559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918559 none CC#CCC(NC(=O)CCNC(=O)CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 11, 11, 11, 11, 11, 11, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 6, 3, 3, 1, 1, 1, 1, 1] 13 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918559 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918559 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918559/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918559 Building REAL300004918560 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918560' /scratch/stefan/7775246/working/building/REAL300004918560 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918560 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918560/0 /scratch/stefan/7775246/working/building/REAL300004918560 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/564 `/scratch/stefan/7775246/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004918560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918560 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918560 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918560 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918560/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918560 Building REAL300004918561 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918561' /scratch/stefan/7775246/working/building/REAL300004918561 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918561 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918561/0 /scratch/stefan/7775246/working/building/REAL300004918561 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/565 `/scratch/stefan/7775246/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C(F)(F)F)C(C)=C1)C(=O)[O-]) `REAL300004918561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918561 none CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C(F)(F)F)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 5, 15, 15, 15, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 5, 11, 11, 11, 22, 22, 22, 1, 1, 1, 17, 28, 28, 59, 59, 59, 59, 59, 17, 5, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [33, 34, 38, 6, 8, 9, 10, 11, 12, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918561 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918561 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918561/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918561 Building REAL300004918562 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918562' /scratch/stefan/7775246/working/building/REAL300004918562 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918562 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918562/0 /scratch/stefan/7775246/working/building/REAL300004918562 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/566 `/scratch/stefan/7775246/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1SCCC2=C1C=CS2)C(=O)[O-]) `REAL300004918562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918562 none CC#CCC(NC(=O)C1SCCC2=C1C=CS2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 45, 45, 72, 72, 72, 72, 72, 31, 10, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918562 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918562 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918562/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918562 Building REAL300004918563 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918563' /scratch/stefan/7775246/working/building/REAL300004918563 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918563 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918563/0 /scratch/stefan/7775246/working/building/REAL300004918563 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/567 `/scratch/stefan/7775246/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNS(=O)(=O)CCOC(C)C)C(=O)[O-]) `REAL300004918563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918563 none CC#CCC(NC(=O)CNS(=O)(=O)CCOC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 9, 5, 5, 5, 5, 1, 1, 1, 4, 4, 4, 7, 7, 9, 12, 12, 9, 12, 12, 13, 13, 13, 13, 13, 9, 5, 5, 5, 1, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 31 rigid atoms, others: [8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918563 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918563 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918563/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918563 Building REAL300004918564 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918564' /scratch/stefan/7775246/working/building/REAL300004918564 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918564 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918564/0 /scratch/stefan/7775246/working/building/REAL300004918564 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/568 `/scratch/stefan/7775246/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2NC(C(F)F)=NC2=C1)C(=O)[O-]) `REAL300004918564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918564 none CC#CCC(NC(=O)C1=CC=C2NC(C(F)F)=NC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 15, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 25, 43, 43, 86, 86, 86, 86, 86, 25, 7, 1, 1, 1, 11, 1] 142 rigid atoms, others: [32, 34, 6, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918564 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918564 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918564/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918564 Building REAL300004918565 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918565' /scratch/stefan/7775246/working/building/REAL300004918565 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918565 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918565/0 /scratch/stefan/7775246/working/building/REAL300004918565 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/569 `/scratch/stefan/7775246/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C(C)(C)C)=N1)C(=O)[O-]) `REAL300004918565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918565 none CC#CCC(NC(=O)CC1=CSC(C(C)(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 60, 36, 36, 8, 36, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 60, 95, 95, 131, 131, 131, 131, 131, 60, 36, 8, 8, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918565 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918565 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918565/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918565 Building REAL300004918566 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918566' /scratch/stefan/7775246/working/building/REAL300004918566 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918566 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918566/0 /scratch/stefan/7775246/working/building/REAL300004918566 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/570 `/scratch/stefan/7775246/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCN(CC1=CC=CC=C1)C(C)=O)C(=O)[O-]) `REAL300004918566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918566 none CC#CCC(NC(=O)CCN(CC1=CC=CC=C1)C(C)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 40, 26, 26, 17, 26, 17, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 40, 49, 49, 58, 58, 58, 58, 58, 40, 26, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 14, 14, 14] 61 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44]) total number of confs: 322 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918566 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918566 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918566/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918566 Building REAL300004918567 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918567' /scratch/stefan/7775246/working/building/REAL300004918567 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918567 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918567/0 /scratch/stefan/7775246/working/building/REAL300004918567 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/571 `/scratch/stefan/7775246/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C2=CC=CC=C2CCCC1=O)C(=O)[O-]) `REAL300004918567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918567 none CC#CCC(NC(=O)CN1C2=CC=CC=C2CCCC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 41, 41, 6, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 135, 135, 201, 201, 201, 201, 201, 101, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 960 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918567 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918567 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918567/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918567 Building REAL300004918568 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918568' /scratch/stefan/7775246/working/building/REAL300004918568 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918568 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918568/0 /scratch/stefan/7775246/working/building/REAL300004918568 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/572 `/scratch/stefan/7775246/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CS(C)(=O)=O)C2=CC=CC=C2O1)C(=O)[O-]) `REAL300004918568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918568 none CC#CCC(NC(=O)C1=C(CS(C)(=O)=O)C2=CC=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1] 5 rigid atoms, others: [37, 6, 39, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918568 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918568 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918568/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918568 Building REAL300004918569 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918569' /scratch/stefan/7775246/working/building/REAL300004918569 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918569 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918569/0 /scratch/stefan/7775246/working/building/REAL300004918569 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/573 `/scratch/stefan/7775246/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918569 none CC#CCC(NC(=O)C(C)(C)C1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 52, 52, 13, 52, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 101, 140, 140, 201, 201, 201, 201, 201, 101, 52, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 983 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918569 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918569 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918569/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918569 Building REAL300004918570 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918570' /scratch/stefan/7775246/working/building/REAL300004918570 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918570 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918570/0 /scratch/stefan/7775246/working/building/REAL300004918570 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/574 `/scratch/stefan/7775246/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC(C)(C)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918570 none CC#CCC(NC(=O)C1CCC(C)(C)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 39, 39, 59, 59, 59, 59, 59, 27, 9, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 59 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 298 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918570 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918570 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918570/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918570 Building REAL300004918571 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918571' /scratch/stefan/7775246/working/building/REAL300004918571 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918571 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918571/0 /scratch/stefan/7775246/working/building/REAL300004918571 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/575 `/scratch/stefan/7775246/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=CC=CC=C1OC)C(=O)[O-]) `REAL300004918571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918571 none CC#CCC(NC(=O)C1CC1C1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 23, 8, 8, 1, 8, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 11, 23, 37, 37, 71, 71, 71, 71, 71, 23, 8, 1, 1, 1, 1, 5, 5, 4, 5, 11, 11, 11] 124 rigid atoms, others: [32, 6, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 351 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918571 none CC#CCC(NC(=O)C1CC1C1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 47, 19, 19, 5, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 47, 70, 70, 104, 104, 104, 104, 104, 47, 19, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4] 124 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 532 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918571 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918571 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918571/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918571 Building REAL300004918572 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918572' /scratch/stefan/7775246/working/building/REAL300004918572 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918572 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918572/0 /scratch/stefan/7775246/working/building/REAL300004918572 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/576 `/scratch/stefan/7775246/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(CC2=CC=C(OC)C=C2)C1)C(=O)[O-]) `REAL300004918572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918572 none CC#CCC(NC(=O)C1CC(=O)N(CC2=CC=C(OC)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 8, 8, 6, 6, 14, 8, 8, 1, 20, 34, 34, 45, 45, 45, 45, 45, 20, 9, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 8, 8, 1, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 46, 45, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918572 none CC#CCC(NC(=O)C1CC(=O)N(CC2=CC=C(OC)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 87, 49, 49, 8, 49, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 3, 1, 1, 8, 87, 136, 136, 158, 158, 158, 158, 158, 87, 49, 8, 8, 8, 4, 4, 1, 1, 3, 3, 3, 1, 1, 8, 8] 201 rigid atoms, others: [38, 39, 43, 44, 13, 14, 15, 16, 17, 18, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 45, 46]) total number of confs: 848 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918572 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918572 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918572/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918572 Building REAL300004918573 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918573' /scratch/stefan/7775246/working/building/REAL300004918573 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918573 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918573/0 /scratch/stefan/7775246/working/building/REAL300004918573 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/577 `/scratch/stefan/7775246/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)N1C=C([N+](=O)[O-])C=N1)C(=O)[O-]) `REAL300004918573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918573 none CC#CCC(NC(=O)C(C)(C)N1C=C([N+](=O)[O-])C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 11, 11, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 125, 61, 61, 11, 61, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 125, 157, 157, 201, 201, 201, 201, 201, 125, 61, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [35, 36, 8, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 940 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918573 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918573 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918573/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918573 Building REAL300004918574 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918574' /scratch/stefan/7775246/working/building/REAL300004918574 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918574 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918574/0 /scratch/stefan/7775246/working/building/REAL300004918574 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/578 `/scratch/stefan/7775246/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCN1N=C(C)C([N+](=O)[O-])=C1C)C(=O)[O-]) `REAL300004918574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918574 none CC#CCC(NC(=O)CCN1N=C(C)C([N+](=O)[O-])=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 8, 1, 5, 1, 8, 11, 11, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 112, 62, 62, 13, 62, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 112, 144, 144, 201, 201, 201, 201, 201, 112, 62, 13, 13, 6, 6, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 994 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918574 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918574 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918574/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918574 Building REAL300004918575 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918575' /scratch/stefan/7775246/working/building/REAL300004918575 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918575 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918575/0 /scratch/stefan/7775246/working/building/REAL300004918575 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/579 `/scratch/stefan/7775246/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2CC2)=N1)C(=O)[O-]) `REAL300004918575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918575 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2CC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 24, 8, 8, 1, 8, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 7, 7, 1, 24, 37, 37, 71, 71, 71, 71, 71, 24, 8, 6, 6, 1, 6, 6, 7, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918575 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2CC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 99, 42, 42, 7, 42, 7, 7, 7, 7, 18, 18, 7, 18, 18, 1, 1, 1, 1, 7, 99, 131, 131, 194, 194, 194, 194, 194, 99, 42, 18, 18, 7, 18, 18, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 935 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918575 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2CC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 68, 28, 28, 6, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 6, 68, 94, 94, 140, 140, 140, 140, 140, 68, 28, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918575 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918575 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918575/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918575 Building REAL300004918576 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918576' /scratch/stefan/7775246/working/building/REAL300004918576 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918576 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918576/0 /scratch/stefan/7775246/working/building/REAL300004918576 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/580 `/scratch/stefan/7775246/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCC1C(=O)N1CCCC1)C(=O)[O-]) `REAL300004918576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918576 none CC#CCC(NC(=O)C1CCCCC1C(=O)N1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 18, 28, 28, 52, 52, 52, 52, 52, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918576 none CC#CCC(NC(=O)C1CCCCC1C(=O)N1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 31, 20, 20, 6, 20, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 31, 42, 42, 59, 59, 59, 59, 59, 31, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [48, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918576 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918576 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918576/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918576 Building REAL300004918577 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918577' /scratch/stefan/7775246/working/building/REAL300004918577 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918577 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918577/0 /scratch/stefan/7775246/working/building/REAL300004918577 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/581 `/scratch/stefan/7775246/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)(CC)C1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918577 none CC#CCC(NC(=O)C(CC)(CC)C1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 44, 24, 24, 6, 24, 1, 6, 7, 6, 8, 1, 1, 1, 1, 1, 1, 1, 44, 60, 60, 81, 81, 81, 81, 81, 44, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 88 rigid atoms, others: [17, 8, 41, 42, 43, 13, 14, 15, 16, 40, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 456 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918577 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918577 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918577/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918577 Building REAL300004918578 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918578' /scratch/stefan/7775246/working/building/REAL300004918578 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918578 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918578/0 /scratch/stefan/7775246/working/building/REAL300004918578 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/582 `/scratch/stefan/7775246/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(C)=C2)CCCC1)C(=O)[O-]) `REAL300004918578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918578 none CC#CCC(NC(=O)C1(C2=CC=CC(C)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 32, 11, 11, 1, 11, 1, 1, 9, 9, 1, 9, 9, 9, 1, 1, 1, 1, 32, 53, 53, 92, 92, 92, 92, 92, 32, 11, 9, 9, 4, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 42, 43, 44, 16, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 472 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918578 none CC#CCC(NC(=O)C1(C2=CC=CC(C)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 84, 33, 33, 9, 33, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 84, 126, 126, 201, 201, 201, 201, 201, 84, 33, 1, 1, 1, 2, 2, 2, 1, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 36, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 993 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918578 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918578 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918578/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918578 Building REAL300004918579 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918579' /scratch/stefan/7775246/working/building/REAL300004918579 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918579 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918579/0 /scratch/stefan/7775246/working/building/REAL300004918579 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/583 `/scratch/stefan/7775246/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C3OCOC3=C2)=N1)C(=O)[O-]) `REAL300004918579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918579 none CC#CCC(NC(=O)C1=CSC(C2=CC=C3OCOC3=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 4, 4, 1, 38, 59, 59, 100, 100, 100, 100, 100, 38, 12, 1, 5, 5, 5, 5, 5] 150 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918579 none CC#CCC(NC(=O)C1=CSC(C2=CC=C3OCOC3=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 87, 40, 40, 4, 40, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 87, 114, 114, 150, 150, 150, 150, 150, 87, 40, 4, 1, 1, 1, 1, 1] 150 rigid atoms, others: [33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918579 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918579 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918579/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918579 Building REAL300004918580 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918580' /scratch/stefan/7775246/working/building/REAL300004918580 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918580 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918580/0 /scratch/stefan/7775246/working/building/REAL300004918580 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/584 `/scratch/stefan/7775246/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC=C1OC(F)(F)F)C(=O)[O-]) `REAL300004918580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918580 none CC#CCC(NC(=O)CCC1=CC=CC=C1OC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 43, 23, 23, 5, 23, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 43, 74, 74, 96, 96, 96, 96, 96, 43, 23, 5, 5, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918580 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918580 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918580/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918580 Building REAL300004918581 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918581' /scratch/stefan/7775246/working/building/REAL300004918581 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918581 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918581/0 /scratch/stefan/7775246/working/building/REAL300004918581 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/585 `/scratch/stefan/7775246/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918581 none CC#CCC(NC(=O)CCC1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 30, 12, 12, 3, 12, 2, 1, 1, 1, 1, 1, 1, 12, 21, 20, 21, 1, 1, 30, 47, 47, 61, 61, 61, 61, 61, 30, 12, 3, 3, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918581 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918581 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918581/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918581 Building REAL300004918582 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918582' /scratch/stefan/7775246/working/building/REAL300004918582 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918582 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918582/0 /scratch/stefan/7775246/working/building/REAL300004918582 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/586 `/scratch/stefan/7775246/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=C(C)C1=CC=CC=C1OC)C(=O)[O-]) `REAL300004918582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918582 none CC#CCC(NC(=O)C=C(C)C1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 108, 45, 45, 7, 45, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 4, 108, 138, 138, 194, 194, 194, 194, 194, 108, 45, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918582 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918582 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918582/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918582 Building REAL300004918583 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918583' /scratch/stefan/7775246/working/building/REAL300004918583 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918583 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918583/0 /scratch/stefan/7775246/working/building/REAL300004918583 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/587 `/scratch/stefan/7775246/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=CO2)S1)C(=O)[O-]) `REAL300004918583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918583 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 34, 52, 52, 85, 85, 85, 85, 85, 34, 13, 1, 11, 11, 11] 149 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918583 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 101, 59, 59, 11, 58, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 101, 118, 118, 149, 149, 149, 149, 149, 101, 59, 11, 1, 1, 1] 149 rigid atoms, others: [11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918583 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918583 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918583/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918583 Building REAL300004918584 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918584' /scratch/stefan/7775246/working/building/REAL300004918584 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918584 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918584/0 /scratch/stefan/7775246/working/building/REAL300004918584 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/588 `/scratch/stefan/7775246/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)CC)=C1)C(=O)[O-]) `REAL300004918584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918584 none CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 17, 1, 13, 21, 21, 31, 31, 31, 31, 31, 13, 5, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918584 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918584 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918584/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918584 Building REAL300004918585 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918585' /scratch/stefan/7775246/working/building/REAL300004918585 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918585 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918585/0 /scratch/stefan/7775246/working/building/REAL300004918585 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/589 `/scratch/stefan/7775246/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2C=CC=C2)C=C1)C(=O)[O-]) `REAL300004918585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918585 none CC#CCC(NC(=O)C1=CC=C(CN2C=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 1, 1, 9, 15, 15, 34, 34, 34, 34, 34, 9, 3, 1, 1, 8, 8, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918585 none CC#CCC(NC(=O)C1=CC=C(CN2C=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 38, 38, 5, 38, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 19, 19, 104, 136, 136, 201, 201, 201, 201, 201, 104, 38, 19, 19, 5, 5, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 984 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918585 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918585 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918585/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918585 Building REAL300004918586 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918586' /scratch/stefan/7775246/working/building/REAL300004918586 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918586 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918586/0 /scratch/stefan/7775246/working/building/REAL300004918586 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/590 `/scratch/stefan/7775246/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C)=C(C2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004918586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918586 none CC#CCC(NC(=O)CCC1=NC(C)=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 125, 86, 87, 21, 87, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 125, 167, 167, 191, 191, 191, 191, 191, 125, 87, 21, 21, 8, 8, 2, 2, 2, 4, 4, 2, 4, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1000 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918586 none CC#CCC(NC(=O)CCC1=NC(C)=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 128, 128, 46, 128, 24, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 163, 190, 190, 201, 201, 201, 201, 201, 163, 128, 46, 46, 24, 24, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 954 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918586 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918586 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918586/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918586 Building REAL300004918587 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918587' /scratch/stefan/7775246/working/building/REAL300004918587 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918587 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918587/0 /scratch/stefan/7775246/working/building/REAL300004918587 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/591 `/scratch/stefan/7775246/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Br)=C2)N=C1)C(=O)[O-]) `REAL300004918587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918587 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Br)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 1, 32, 42, 42, 67, 67, 67, 67, 67, 32, 11, 2, 2, 2, 5, 5, 4, 5, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 323 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918587 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Br)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 45, 45, 5, 45, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 105, 140, 140, 201, 201, 201, 201, 201, 105, 45, 5, 5, 5, 1, 1, 1, 1, 5] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 966 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918587 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918587 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918587/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918587 Building REAL300004918588 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918588' /scratch/stefan/7775246/working/building/REAL300004918588 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918588 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918588/0 /scratch/stefan/7775246/working/building/REAL300004918588 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/592 `/scratch/stefan/7775246/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(Br)=C2)C=C1)C(=O)[O-]) `REAL300004918588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918588 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Br)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 36, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 6, 6, 7, 6, 1, 1, 36, 55, 55, 89, 89, 89, 89, 89, 36, 11, 7, 7, 6, 7, 1, 1] 152 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918588 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Br)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 90, 43, 43, 6, 42, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 90, 115, 115, 152, 152, 152, 152, 152, 90, 43, 1, 1, 1, 1, 7, 6] 152 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 689 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918588 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918588 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918588/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918588 Building REAL300004918589 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918589' /scratch/stefan/7775246/working/building/REAL300004918589 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918589 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918589/0 /scratch/stefan/7775246/working/building/REAL300004918589 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/593 `/scratch/stefan/7775246/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)NC2=CC=NN2C1=O)C(=O)[O-]) `REAL300004918589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918589 none CC#CCC(NC(=O)CC1=C(C)NC2=CC=NN2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 91, 28, 28, 5, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 124, 124, 198, 198, 198, 198, 198, 91, 28, 5, 5, 2, 2, 2, 1, 1, 1] 198 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 925 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918589 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918589 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918589/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918589 Building REAL300004918590 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918590' /scratch/stefan/7775246/working/building/REAL300004918590 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918590 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918590/0 /scratch/stefan/7775246/working/building/REAL300004918590 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/594 `/scratch/stefan/7775246/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-]) `REAL300004918590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918590 none CC#CCC(NC(=O)CC1=COC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 93, 43, 43, 7, 43, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 93, 138, 138, 197, 197, 197, 197, 197, 93, 43, 7, 7, 1, 4, 4, 4, 4] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 1011 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918590 none CC#CCC(NC(=O)CC1=COC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 73, 73, 16, 73, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 119, 156, 156, 201, 201, 201, 201, 201, 119, 73, 16, 16, 4, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 990 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918590 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918590 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918590/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918590 Building REAL300004918591 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918591' /scratch/stefan/7775246/working/building/REAL300004918591 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918591 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918591/0 /scratch/stefan/7775246/working/building/REAL300004918591 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/595 `/scratch/stefan/7775246/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(OC(F)F)C=CS1)C(=O)[O-]) `REAL300004918591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918591 none CC#CCC(NC(=O)C1=C(OC(F)F)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 15, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 5, 5, 5, 1, 5, 1, 1, 1, 3, 5, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1] 7 rigid atoms, others: [6, 8, 9, 10, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918591 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918591 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918591/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918591 Building REAL300004918592 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918592' /scratch/stefan/7775246/working/building/REAL300004918592 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918592 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918592/0 /scratch/stefan/7775246/working/building/REAL300004918592 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/596 `/scratch/stefan/7775246/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC(OCC)=C1OC1CCCC1)C(=O)[O-]) `REAL300004918592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918592 none CC#CCC(NC(=O)C=CC1=CC=CC(OCC)=C1OC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 41, 27, 28, 9, 28, 9, 1, 1, 1, 1, 1, 1, 1, 8, 20, 1, 1, 5, 9, 9, 9, 9, 41, 56, 56, 89, 89, 89, 89, 89, 41, 28, 9, 9, 1, 1, 1, 20, 20, 21, 21, 21, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918592 none CC#CCC(NC(=O)C=CC1=CC=CC(OCC)=C1OC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 97, 77, 77, 39, 77, 39, 9, 9, 9, 7, 9, 9, 9, 22, 33, 5, 1, 1, 1, 1, 1, 1, 97, 119, 119, 151, 151, 151, 151, 151, 97, 77, 39, 39, 9, 9, 9, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918592 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918592 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918592/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918592 Building REAL300004918593 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918593' /scratch/stefan/7775246/working/building/REAL300004918593 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918593 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918593/0 /scratch/stefan/7775246/working/building/REAL300004918593 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/597 `/scratch/stefan/7775246/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(OC1=CC=C(F)C(F)=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918593 none CC#CCC(NC(=O)C(OC1=CC=C(F)C(F)=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 112, 71, 71, 24, 71, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 33, 33, 33, 33, 33, 112, 149, 149, 189, 189, 189, 189, 189, 112, 71, 24, 1, 1, 1, 33, 33, 33, 33, 33] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 974 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918593 none CC#CCC(NC(=O)C(OC1=CC=C(F)C(F)=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 26, 11, 11, 4, 11, 1, 4, 9, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 26, 42, 42, 49, 49, 49, 49, 49, 26, 11, 4, 33, 33, 33, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 8, 41, 42, 40, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 311 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918593 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918593 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918593/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918593 Building REAL300004918594 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918594' /scratch/stefan/7775246/working/building/REAL300004918594 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918594 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918594/0 /scratch/stefan/7775246/working/building/REAL300004918594 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/598 `/scratch/stefan/7775246/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(Cl)=C2)C=C1)C(=O)[O-]) `REAL300004918594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918594 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 36, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 36, 52, 52, 87, 87, 87, 87, 87, 36, 11, 6, 6, 6, 1, 1] 148 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918594 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 85, 41, 41, 6, 40, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 85, 109, 109, 148, 148, 148, 148, 148, 85, 41, 1, 1, 1, 6, 6] 148 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918594 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918594 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918594/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918594 Building REAL300004918595 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918595' /scratch/stefan/7775246/working/building/REAL300004918595 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918595 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918595/0 /scratch/stefan/7775246/working/building/REAL300004918595 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/599 `/scratch/stefan/7775246/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)C(C)=C2)C=C1F)C(=O)[O-]) `REAL300004918595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918595 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)C(C)=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 5, 5, 1, 1, 1, 30, 41, 41, 59, 59, 59, 59, 59, 30, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 44, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 295 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918595 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)C(C)=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 43, 43, 5, 43, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 108, 142, 142, 201, 201, 201, 201, 201, 108, 43, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5] 201 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 970 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918595 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918595 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918595/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918595 Building REAL300004918596 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918596' /scratch/stefan/7775246/working/building/REAL300004918596 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918596 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918596/0 /scratch/stefan/7775246/working/building/REAL300004918596 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/600 `/scratch/stefan/7775246/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC)C=C2)C=C1F)C(=O)[O-]) `REAL300004918596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918596 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC)C=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 42, 13, 13, 1, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 1, 1, 1, 42, 66, 66, 109, 109, 109, 109, 109, 42, 13, 1, 1, 3, 3, 5, 5, 5, 3, 3, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 534 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918596 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC)C=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 71, 25, 25, 3, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 3, 3, 3, 71, 110, 110, 165, 165, 165, 165, 165, 71, 25, 3, 3, 1, 1, 2, 2, 2, 1, 1, 3] 201 rigid atoms, others: [35, 36, 40, 41, 11, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42]) total number of confs: 816 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918596 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918596 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918596/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918596 Building REAL300004918597 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918597' /scratch/stefan/7775246/working/building/REAL300004918597 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918597 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918597/0 /scratch/stefan/7775246/working/building/REAL300004918597 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/601 `/scratch/stefan/7775246/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)C=C1F)C(=O)[O-]) `REAL300004918597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918597 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 49, 13, 13, 1, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 1, 49, 70, 70, 114, 114, 114, 114, 114, 49, 13, 1, 1, 3, 3, 3, 3, 1] 128 rigid atoms, others: [32, 33, 38, 6, 8, 9, 10, 11, 12, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 538 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918597 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 72, 24, 24, 3, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 72, 93, 93, 128, 128, 128, 128, 128, 72, 24, 3, 3, 1, 1, 1, 1, 3] 128 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 599 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918597 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918597 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918597/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918597 Building REAL300004918598 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918598' /scratch/stefan/7775246/working/building/REAL300004918598 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918598 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918598/0 /scratch/stefan/7775246/working/building/REAL300004918598 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/602 `/scratch/stefan/7775246/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)C=C2)C=C1F)C(=O)[O-]) `REAL300004918598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918598 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)C=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 48, 13, 13, 1, 13, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 1, 1, 48, 68, 68, 112, 112, 112, 112, 112, 48, 13, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1] 126 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918598 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)C=C2)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 69, 24, 24, 3, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 69, 90, 90, 126, 126, 126, 126, 126, 69, 24, 3, 3, 1, 1, 2, 2, 2, 1, 1, 3] 126 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41]) total number of confs: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918598 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918598 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918598/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918598 Building REAL300004918599 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918599' /scratch/stefan/7775246/working/building/REAL300004918599 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918599 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918599/0 /scratch/stefan/7775246/working/building/REAL300004918599 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/603 `/scratch/stefan/7775246/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(=O)C2=CC(Br)=CC=C2N1)C(=O)[O-]) `REAL300004918599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918599 none CC#CCC(NC(=O)C1=CC(=O)C2=CC(Br)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 42, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 56, 56, 82, 82, 82, 82, 82, 42, 12, 1, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 378 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918599 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918599 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918599/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918599 Building REAL300004918600 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918600' /scratch/stefan/7775246/working/building/REAL300004918600 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918600 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918600/0 /scratch/stefan/7775246/working/building/REAL300004918600 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/604 `/scratch/stefan/7775246/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=C(CC)C=C2)=N1)C(=O)[O-]) `REAL300004918600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918600 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(CC)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 53, 29, 29, 8, 29, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 7, 4, 4, 1, 53, 80, 80, 89, 89, 89, 89, 89, 53, 29, 8, 8, 1, 4, 4, 7, 7, 7, 7, 7, 4, 4] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918600 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(CC)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 83, 49, 49, 18, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 83, 103, 103, 109, 109, 109, 109, 109, 83, 49, 18, 18, 4, 1, 1, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [35, 36, 42, 43, 12, 13, 14, 15, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918600 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918600 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918600/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918600 Building REAL300004918601 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918601' /scratch/stefan/7775246/working/building/REAL300004918601 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918601 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918601/0 /scratch/stefan/7775246/working/building/REAL300004918601 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/605 `/scratch/stefan/7775246/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918601 none CC#CCC(NC(=O)C(C)OC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 66, 66, 12, 66, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 120, 157, 157, 201, 201, 201, 201, 201, 120, 66, 12, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 983 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918601 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918601 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918601/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918601 Building REAL300004918602 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918602' /scratch/stefan/7775246/working/building/REAL300004918602 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918602 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918602/0 /scratch/stefan/7775246/working/building/REAL300004918602 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/606 `/scratch/stefan/7775246/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004918602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918602 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 41, 41, 7, 41, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 98, 132, 132, 201, 201, 201, 201, 201, 98, 41, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 937 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918602 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918602 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918602/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918602 Building REAL300004918603 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918603' /scratch/stefan/7775246/working/building/REAL300004918603 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918603 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918603/0 /scratch/stefan/7775246/working/building/REAL300004918603 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/607 `/scratch/stefan/7775246/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)ON=C1C1=C(Cl)C=CC=C1Cl)C(=O)[O-]) `REAL300004918603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918603 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=C(Cl)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 46, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 2, 4, 4, 4, 46, 71, 71, 115, 115, 115, 115, 115, 46, 13, 2, 2, 2, 4, 2, 4] 132 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918603 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=C(Cl)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 78, 31, 31, 5, 31, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 99, 99, 132, 132, 132, 132, 132, 78, 31, 5, 5, 5, 1, 1, 1] 132 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918603 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918603 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918603/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918603 Building REAL300004918604 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918604' /scratch/stefan/7775246/working/building/REAL300004918604 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918604 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918604/0 /scratch/stefan/7775246/working/building/REAL300004918604 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/608 `/scratch/stefan/7775246/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C=CS1)C(=O)[O-]) `REAL300004918604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918604 none CC#CCC(NC(=O)C1=C(Br)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 24, 37, 37, 47, 47, 47, 47, 47, 24, 5, 1, 1] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918604 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918604 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918604/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918604 Building REAL300004918605 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918605' /scratch/stefan/7775246/working/building/REAL300004918605 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918605 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918605/0 /scratch/stefan/7775246/working/building/REAL300004918605 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/609 `/scratch/stefan/7775246/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(OC)C=C2)CCCC1)C(=O)[O-]) `REAL300004918605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918605 none CC#CCC(NC(=O)C1(C2=CC=C(OC)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 36, 11, 11, 1, 11, 1, 1, 5, 5, 1, 1, 9, 5, 5, 1, 1, 1, 1, 36, 58, 58, 113, 113, 113, 113, 113, 36, 11, 5, 5, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 38, 6, 39, 8, 9, 42, 43, 44, 17, 18, 19, 20, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 545 number of broken/clashed sets: 181 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918605 none CC#CCC(NC(=O)C1(C2=CC=C(OC)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 55, 19, 19, 5, 19, 1, 1, 1, 1, 1, 1, 2, 1, 1, 5, 5, 5, 5, 55, 87, 87, 146, 146, 146, 146, 146, 55, 19, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 712 number of broken/clashed sets: 181 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918605 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918605 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918605/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918605 Building REAL300004918606 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918606' /scratch/stefan/7775246/working/building/REAL300004918606 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918606 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918606/0 /scratch/stefan/7775246/working/building/REAL300004918606 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/610 `/scratch/stefan/7775246/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004918606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918606 none CC#CCC(NC(=O)CCCC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 59, 24, 24, 8, 24, 4, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 59, 98, 98, 139, 139, 139, 139, 139, 59, 24, 8, 8, 4, 4, 2, 2, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918606 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918606 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918606/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918606 Building REAL300004918607 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918607' /scratch/stefan/7775246/working/building/REAL300004918607 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918607 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918607/0 /scratch/stefan/7775246/working/building/REAL300004918607 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/611 `/scratch/stefan/7775246/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2Cl)=NN1)C(=O)[O-]) `REAL300004918607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918607 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2Cl)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 33, 10, 10, 1, 10, 1, 1, 1, 1, 10, 10, 9, 10, 10, 10, 1, 1, 33, 52, 52, 79, 79, 79, 79, 79, 33, 11, 1, 10, 10, 9, 10, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918607 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2Cl)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 55, 55, 10, 55, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 118, 146, 146, 201, 201, 201, 201, 201, 118, 55, 10, 1, 1, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 912 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918607 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918607 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918607/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918607 Building REAL300004918608 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918608' /scratch/stefan/7775246/working/building/REAL300004918608 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918608 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918608/0 /scratch/stefan/7775246/working/building/REAL300004918608 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/612 `/scratch/stefan/7775246/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC([N+](=O)[O-])=C2N1)C(=O)[O-]) `REAL300004918608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918608 none CC#CCC(NC(=O)C1=CC2=CC=CC([N+](=O)[O-])=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 51, 51, 71, 71, 71, 71, 71, 36, 12, 1, 1, 1, 1, 1] 71 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918608 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918608 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918608/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918608 Building REAL300004918609 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918609' /scratch/stefan/7775246/working/building/REAL300004918609 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918609 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918609/0 /scratch/stefan/7775246/working/building/REAL300004918609 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/613 `/scratch/stefan/7775246/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(F)C=C2)=NN1)C(=O)[O-]) `REAL300004918609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918609 none CC#CCC(NC(=O)C1=CC(C2=CC=C(F)C=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 42, 12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 42, 67, 67, 104, 104, 104, 104, 104, 42, 13, 1, 7, 7, 7, 7, 1] 140 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918609 none CC#CCC(NC(=O)C1=CC(C2=CC=C(F)C=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 102, 54, 54, 7, 54, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 102, 120, 120, 140, 140, 140, 140, 140, 102, 54, 7, 1, 1, 1, 1, 7] 140 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 606 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918609 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918609 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918609/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918609 Building REAL300004918610 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918610' /scratch/stefan/7775246/working/building/REAL300004918610 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918610 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918610/0 /scratch/stefan/7775246/working/building/REAL300004918610 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/614 `/scratch/stefan/7775246/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918610 none CC#CCC(NC(=O)CC1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 21, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 12, 14, 14, 14, 1, 1, 21, 30, 30, 48, 48, 48, 48, 48, 21, 9, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918610 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918610 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918610/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918610 Building REAL300004918611 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918611' /scratch/stefan/7775246/working/building/REAL300004918611 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918611 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918611/0 /scratch/stefan/7775246/working/building/REAL300004918611 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/615 `/scratch/stefan/7775246/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(S(=O)(=O)C2=CC=C(C)C=C2)C=C1)C(=O)[O-]) `REAL300004918611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918611 none CC#CCC(NC(=O)C1=CN(S(=O)(=O)C2=CC=C(C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 17, 5, 5, 1, 5, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 11, 12, 1, 1, 17, 26, 26, 43, 43, 43, 43, 43, 17, 5, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918611 none CC#CCC(NC(=O)C1=CN(S(=O)(=O)C2=CC=C(C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 41, 41, 12, 41, 12, 12, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 111, 149, 149, 201, 201, 201, 201, 201, 111, 41, 12, 1, 1, 2, 2, 2, 1, 1, 12, 12] 201 rigid atoms, others: [34, 35, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918611 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918611 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918611/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918611 Building REAL300004918612 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918612' /scratch/stefan/7775246/working/building/REAL300004918612 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918612 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918612/0 /scratch/stefan/7775246/working/building/REAL300004918612 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/616 `/scratch/stefan/7775246/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918612 none CC#CCC(NC(=O)COC1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 80, 80, 16, 80, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 125, 161, 161, 201, 201, 201, 201, 201, 125, 80, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1005 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918612 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918612 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918612/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918612 Building REAL300004918613 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918613' /scratch/stefan/7775246/working/building/REAL300004918613 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918613 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918613/0 /scratch/stefan/7775246/working/building/REAL300004918613 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/617 `/scratch/stefan/7775246/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918613 none CC#CCC(NC(=O)C(C)OC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 59, 59, 14, 59, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 109, 150, 150, 201, 201, 201, 201, 201, 109, 59, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1003 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918613 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918613 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918613/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918613 Building REAL300004918614 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918614' /scratch/stefan/7775246/working/building/REAL300004918614 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918614 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918614/0 /scratch/stefan/7775246/working/building/REAL300004918614 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/618 `/scratch/stefan/7775246/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1C)C(=O)[O-]) `REAL300004918614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918614 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 34, 49, 49, 71, 71, 71, 71, 71, 34, 10, 1, 1, 1, 2, 2, 2] 71 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918614 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918614 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918614/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918614 Building REAL300004918615 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918615' /scratch/stefan/7775246/working/building/REAL300004918615 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918615 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918615/0 /scratch/stefan/7775246/working/building/REAL300004918615 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/619 `/scratch/stefan/7775246/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SC(F)(F)F)C(=O)[O-]) `REAL300004918615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918615 none CC#CCC(NC(=O)C1=CC=CC=C1SC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918615 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918615 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918615/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918615 Building REAL300004918616 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918616' /scratch/stefan/7775246/working/building/REAL300004918616 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918616 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918616/0 /scratch/stefan/7775246/working/building/REAL300004918616 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/620 `/scratch/stefan/7775246/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC(Cl)=C2)=NN1)C(=O)[O-]) `REAL300004918616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918616 none CC#CCC(NC(=O)C1=CC(C2=CC=CC(Cl)=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 28, 9, 9, 1, 9, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 1, 1, 28, 45, 45, 68, 68, 68, 68, 68, 28, 9, 1, 13, 13, 12, 13, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918616 none CC#CCC(NC(=O)C1=CC(C2=CC=CC(Cl)=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 73, 73, 13, 73, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 141, 166, 166, 201, 201, 201, 201, 201, 141, 73, 13, 1, 1, 1, 1, 13] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918616 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918616 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918616/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918616 Building REAL300004918617 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918617' /scratch/stefan/7775246/working/building/REAL300004918617 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918617 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918617/0 /scratch/stefan/7775246/working/building/REAL300004918617 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/621 `/scratch/stefan/7775246/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1Cl)C(=O)[O-]) `REAL300004918617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918617 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 30, 30, 54, 54, 54, 54, 54, 22, 7, 1, 1, 1] 54 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918617 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918617 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918617/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918617 Building REAL300004918618 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918618' /scratch/stefan/7775246/working/building/REAL300004918618 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918618 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918618/0 /scratch/stefan/7775246/working/building/REAL300004918618 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/622 `/scratch/stefan/7775246/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1)C(=O)[O-]) `REAL300004918618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918618 none CC#CCC(NC(=O)C1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 13, 18, 18, 36, 36, 36, 36, 36, 13, 4, 1, 1, 7, 7, 1, 1] 81 rigid atoms, others: [33, 34, 37, 6, 8, 9, 10, 11, 12, 21, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918618 none CC#CCC(NC(=O)C1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 43, 15, 15, 2, 15, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 43, 55, 55, 81, 81, 81, 81, 81, 43, 15, 7, 7, 1, 1, 7, 7] 81 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918618 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918618 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918618/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918618 Building REAL300004918619 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918619' /scratch/stefan/7775246/working/building/REAL300004918619 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918619 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918619/0 /scratch/stefan/7775246/working/building/REAL300004918619 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/623 `/scratch/stefan/7775246/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC(Br)=C1)C(=O)[O-]) `REAL300004918619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918619 none CC#CCC(NC(=O)C1=CC(F)=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 25, 40, 40, 73, 73, 73, 73, 73, 25, 7, 1, 1, 1] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918619 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918619 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918619/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918619 Building REAL300004918620 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918620' /scratch/stefan/7775246/working/building/REAL300004918620 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918620 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918620/0 /scratch/stefan/7775246/working/building/REAL300004918620 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/624 `/scratch/stefan/7775246/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918620 none CC#CCC(NC(=O)COC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 60, 41, 41, 12, 41, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 60, 62, 62, 66, 66, 66, 66, 66, 60, 41, 12, 12, 1, 1, 1, 1] 66 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 260 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918620 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918620 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918620/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918620 Building REAL300004918621 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918621' /scratch/stefan/7775246/working/building/REAL300004918621 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918621 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918621/0 /scratch/stefan/7775246/working/building/REAL300004918621 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/625 `/scratch/stefan/7775246/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)C2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004918621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918621 none CC#CCC(NC(=O)C1CCN(C(=O)C2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 1, 1, 28, 45, 45, 73, 73, 73, 73, 73, 28, 11, 1, 1, 1, 1, 1, 11, 11, 8, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 44, 43, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918621 none CC#CCC(NC(=O)C1CCN(C(=O)C2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 60, 60, 11, 60, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 111, 151, 151, 201, 201, 201, 201, 201, 111, 60, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918621 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918621 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918621/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918621 Building REAL300004918622 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918622' /scratch/stefan/7775246/working/building/REAL300004918622 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918622 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918622/0 /scratch/stefan/7775246/working/building/REAL300004918622 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/626 `/scratch/stefan/7775246/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OC(F)F)=C1)C(=O)[O-]) `REAL300004918622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918622 none CC#CCC(NC(=O)CC1=CC=CC(OC(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 31, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 1, 12, 17, 17, 1, 31, 47, 47, 62, 62, 62, 62, 62, 31, 15, 6, 6, 1, 1, 1, 17, 1] 201 rigid atoms, others: [32, 33, 35, 8, 9, 10, 11, 12, 13, 14, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918622 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918622 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918622/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918622 Building REAL300004918623 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918623' /scratch/stefan/7775246/working/building/REAL300004918623 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918623 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918623/0 /scratch/stefan/7775246/working/building/REAL300004918623 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/627 `/scratch/stefan/7775246/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC=C(F)C=C12)C(=O)[O-]) `REAL300004918623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918623 none CC#CCC(NC(=O)CC1=CNC2=CC=C(F)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 95, 48, 48, 8, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 140, 140, 201, 201, 201, 201, 201, 95, 48, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1004 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918623 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918623 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918623/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918623 Building REAL300004918624 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918624' /scratch/stefan/7775246/working/building/REAL300004918624 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918624 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918624/0 /scratch/stefan/7775246/working/building/REAL300004918624 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/628 `/scratch/stefan/7775246/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=CC=C1OC)C(=O)[O-]) `REAL300004918624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918624 none CC#CCC(NC(=O)C=CC1=CC(Cl)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 89, 53, 53, 9, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 89, 130, 130, 181, 181, 181, 181, 181, 89, 53, 9, 9, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 884 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918624 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918624 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918624/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918624 Building REAL300004918625 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918625' /scratch/stefan/7775246/working/building/REAL300004918625 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918625 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918625/0 /scratch/stefan/7775246/working/building/REAL300004918625 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/629 `/scratch/stefan/7775246/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC=C1OC(F)F)C(=O)[O-]) `REAL300004918625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918625 none CC#CCC(NC(=O)CC1=CC=CC=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 52, 30, 30, 5, 30, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 52, 81, 81, 110, 110, 110, 110, 110, 52, 30, 5, 5, 1, 1, 1, 1, 27] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918625 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918625 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918625/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918625 Building REAL300004918626 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918626' /scratch/stefan/7775246/working/building/REAL300004918626 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918626 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918626/0 /scratch/stefan/7775246/working/building/REAL300004918626 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/630 `/scratch/stefan/7775246/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004918626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918626 none CC#CCC(NC(=O)CCC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 50, 50, 10, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 106, 142, 142, 201, 201, 201, 201, 201, 106, 50, 10, 10, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 974 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918626 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918626 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918626/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918626 Building REAL300004918627 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918627' /scratch/stefan/7775246/working/building/REAL300004918627 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918627 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918627/0 /scratch/stefan/7775246/working/building/REAL300004918627 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/631 `/scratch/stefan/7775246/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)ON=C1C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918627 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 57, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 57, 93, 93, 156, 156, 156, 156, 156, 57, 12, 2, 2, 2, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918627 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 43, 43, 7, 43, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 110, 145, 145, 201, 201, 201, 201, 201, 110, 43, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 929 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918627 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918627 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918627/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918627 Building REAL300004918628 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918628' /scratch/stefan/7775246/working/building/REAL300004918628 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918628 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918628/0 /scratch/stefan/7775246/working/building/REAL300004918628 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/632 `/scratch/stefan/7775246/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004918628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918628 none CC#CCC(NC(=O)CC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 39, 39, 6, 39, 1, 1, 1, 1, 1, 1, 1, 1, 93, 135, 135, 201, 201, 201, 201, 201, 93, 39, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 980 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918628 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918628 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918628/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918628 Building REAL300004918629 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918629' /scratch/stefan/7775246/working/building/REAL300004918629 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918629 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918629/0 /scratch/stefan/7775246/working/building/REAL300004918629 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/633 `/scratch/stefan/7775246/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(Br)=C1C)C(=O)[O-]) `REAL300004918629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918629 none CC#CCC(NC(=O)C1=CC=CC(Br)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 39, 51, 51, 78, 78, 78, 78, 78, 39, 10, 1, 1, 1, 2, 2, 2] 78 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918629 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918629 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918629/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918629 Building REAL300004918630 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918630' /scratch/stefan/7775246/working/building/REAL300004918630 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918630 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918630/0 /scratch/stefan/7775246/working/building/REAL300004918630 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/634 `/scratch/stefan/7775246/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC(F)=CC=C12)C(=O)[O-]) `REAL300004918630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918630 none CC#CCC(NC(=O)CC1=CNC2=CC(F)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 97, 49, 49, 8, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 137, 137, 201, 201, 201, 201, 201, 97, 49, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 989 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918630 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918630 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918630/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918630 Building REAL300004918631 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918631' /scratch/stefan/7775246/working/building/REAL300004918631 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918631 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918631/0 /scratch/stefan/7775246/working/building/REAL300004918631 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/635 `/scratch/stefan/7775246/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=CC=C2)C1)C(=O)[O-]) `REAL300004918631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918631 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 11, 16, 16, 1, 22, 35, 35, 54, 54, 54, 54, 54, 22, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 13, 16, 16, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 46, 45, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918631 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 83, 83, 16, 83, 16, 16, 16, 16, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 16, 128, 162, 162, 201, 201, 201, 201, 201, 128, 83, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16] 201 rigid atoms, others: [40, 41, 42, 43, 44, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 922 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918631 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918631 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918631/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918631 Building REAL300004918632 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918632' /scratch/stefan/7775246/working/building/REAL300004918632 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918632 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918632/0 /scratch/stefan/7775246/working/building/REAL300004918632 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/636 `/scratch/stefan/7775246/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004918632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918632 none CC#CCC(NC(=O)CCC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 105, 51, 51, 10, 51, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 141, 141, 201, 201, 201, 201, 201, 105, 51, 10, 10, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 980 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918632 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918632 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918632/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918632 Building REAL300004918633 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918633' /scratch/stefan/7775246/working/building/REAL300004918633 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918633 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918633/0 /scratch/stefan/7775246/working/building/REAL300004918633 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/637 `/scratch/stefan/7775246/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNS(=O)(=O)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918633 none CC#CCC(NC(=O)CNS(=O)(=O)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 87, 48, 48, 15, 48, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 112, 112, 112, 112, 112, 87, 48, 15, 15, 9, 1, 1, 1, 1] 112 rigid atoms, others: [36, 37, 38, 39, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918633 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918633 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918633/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918633 Building REAL300004918634 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918634' /scratch/stefan/7775246/working/building/REAL300004918634 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918634 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918634/0 /scratch/stefan/7775246/working/building/REAL300004918634 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/638 `/scratch/stefan/7775246/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918634 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 38, 12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 6, 6, 1, 6, 6, 1, 38, 61, 61, 106, 106, 106, 106, 106, 38, 12, 6, 6, 3, 6, 6, 6, 6, 1, 6, 6] 191 rigid atoms, others: [6, 8, 9, 10, 11, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918634 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 93, 40, 40, 6, 40, 6, 6, 6, 6, 14, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 6, 93, 124, 124, 191, 191, 191, 191, 191, 93, 40, 14, 14, 8, 14, 14, 1, 1, 1, 1, 1] 191 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 910 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918634 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 107, 43, 43, 6, 43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 7, 14, 14, 6, 107, 137, 137, 189, 189, 189, 189, 189, 107, 43, 1, 1, 1, 1, 1, 14, 14, 7, 14, 14] 191 rigid atoms, others: [35, 36, 37, 38, 39, 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, 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 /scratch/stefan/7775246/working/building/REAL300004918634 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918634 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918634/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918634 Building REAL300004918635 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918635' /scratch/stefan/7775246/working/building/REAL300004918635 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918635 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918635/0 /scratch/stefan/7775246/working/building/REAL300004918635 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/639 `/scratch/stefan/7775246/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004918635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918635 none CC#CCC(NC(=O)C=CC1=CC=C(OCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 27, 24, 24, 5, 24, 5, 1, 1, 1, 1, 1, 1, 9, 28, 46, 1, 1, 9, 15, 1, 27, 27, 27, 34, 34, 34, 34, 34, 27, 24, 5, 5, 1, 1, 28, 28, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 49, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918635 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918635 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918635/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918635 Building REAL300004918636 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918636' /scratch/stefan/7775246/working/building/REAL300004918636 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918636 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918636/0 /scratch/stefan/7775246/working/building/REAL300004918636 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/640 `/scratch/stefan/7775246/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004918636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918636 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 33, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 12, 12, 8, 12, 12, 1, 1, 1, 33, 50, 50, 63, 63, 63, 63, 63, 33, 12, 2, 2, 2, 5, 5, 12, 12, 11, 12, 12, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 377 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918636 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 69, 69, 12, 69, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 130, 162, 162, 201, 201, 201, 201, 201, 130, 69, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44]) total number of confs: 957 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918636 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918636 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918636/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918636 Building REAL300004918637 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918637' /scratch/stefan/7775246/working/building/REAL300004918637 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918637 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918637/0 /scratch/stefan/7775246/working/building/REAL300004918637 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/641 `/scratch/stefan/7775246/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC(=O)C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004918637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918637 none CC#CCC(NC(=O)CCNC(=O)C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 22, 19, 19, 9, 19, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 24, 24, 24, 24, 24, 22, 19, 9, 9, 9, 9, 3, 1, 1, 1, 1] 24 rigid atoms, others: [37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918637 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918637 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918637/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918637 Building REAL300004918638 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918638' /scratch/stefan/7775246/working/building/REAL300004918638 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918638 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918638/0 /scratch/stefan/7775246/working/building/REAL300004918638 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/642 `/scratch/stefan/7775246/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CNC2=CC=CC=C12)NC(C)=O)C(=O)[O-]) `REAL300004918638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918638 none CC#CCC(NC(=O)C(CC1=CNC2=CC=CC=C12)NC(C)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 66, 45, 45, 15, 45, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 23, 66, 66, 66, 84, 84, 84, 84, 84, 66, 45, 15, 5, 5, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 84 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918638 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918638 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918638/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918638 Building REAL300004918639 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918639' /scratch/stefan/7775246/working/building/REAL300004918639 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918639 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918639/0 /scratch/stefan/7775246/working/building/REAL300004918639 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/643 `/scratch/stefan/7775246/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-]) `REAL300004918639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918639 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 5, 15, 15, 10, 15, 15, 15, 1, 1, 1, 18, 30, 30, 37, 37, 37, 37, 37, 18, 10, 2, 2, 2, 5, 5, 15, 15, 14, 15, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 266 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918639 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 72, 72, 15, 72, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 126, 161, 161, 201, 201, 201, 201, 201, 126, 72, 15, 15, 15, 6, 6, 1, 1, 1, 1, 15, 15, 15] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 1001 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918639 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918639 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918639/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918639 Building REAL300004918640 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918640' /scratch/stefan/7775246/working/building/REAL300004918640 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918640 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918640/0 /scratch/stefan/7775246/working/building/REAL300004918640 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/644 `/scratch/stefan/7775246/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(CC(C)C)C(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004918640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918640 none CC#CCC(NC(=O)C1=NN(CC(C)C)C(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 35, 9, 9, 1, 9, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 53, 53, 90, 90, 90, 90, 90, 35, 9, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [43, 6, 8, 9, 10, 11, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918640 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918640 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918640/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918640 Building REAL300004918641 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918641' /scratch/stefan/7775246/working/building/REAL300004918641 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918641 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918641/0 /scratch/stefan/7775246/working/building/REAL300004918641 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/645 `/scratch/stefan/7775246/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C3OCCOC3=C2)C1)C(=O)[O-]) `REAL300004918641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918641 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C3OCCOC3=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 11, 11, 10, 11, 11, 11, 11, 11, 11, 1, 33, 56, 56, 67, 67, 67, 67, 67, 33, 10, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 44, 23, 45] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 373 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918641 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C3OCCOC3=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 56, 56, 11, 56, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 132, 165, 165, 201, 201, 201, 201, 201, 132, 56, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45]) total number of confs: 949 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918641 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918641 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918641/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918641 Building REAL300004918642 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918642' /scratch/stefan/7775246/working/building/REAL300004918642 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918642 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918642/0 /scratch/stefan/7775246/working/building/REAL300004918642 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/646 `/scratch/stefan/7775246/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC2=CC(C)=C(C(C)C)C=C12)C(=O)[O-]) `REAL300004918642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918642 none CC#CCC(NC(=O)CC1=COC2=CC(C)=C(C(C)C)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 5, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 52, 52, 8, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 109, 149, 149, 201, 201, 201, 201, 201, 109, 52, 8, 8, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1007 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918642 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918642 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918642/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918642 Building REAL300004918643 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918643' /scratch/stefan/7775246/working/building/REAL300004918643 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918643 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918643/0 /scratch/stefan/7775246/working/building/REAL300004918643 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/647 `/scratch/stefan/7775246/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC2=C1C1=C(C=CC=C1)C=C2)C(=O)[O-]) `REAL300004918643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918643 none CC#CCC(NC(=O)CC1=COC2=C1C1=C(C=CC=C1)C=C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 98, 43, 43, 6, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 137, 137, 201, 201, 201, 201, 201, 98, 43, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 33, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 982 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918643 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918643 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918643/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918643 Building REAL300004918644 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918644' /scratch/stefan/7775246/working/building/REAL300004918644 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918644 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918644/0 /scratch/stefan/7775246/working/building/REAL300004918644 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/648 `/scratch/stefan/7775246/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(I)C=C1)C(=O)[O-]) `REAL300004918644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918644 none CC#CCC(NC(=O)COC1=CC=C(I)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 65, 65, 14, 65, 4, 1, 1, 1, 1, 1, 1, 1, 1, 117, 153, 153, 201, 201, 201, 201, 201, 117, 65, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 978 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918644 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918644 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918644/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918644 Building REAL300004918645 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918645' /scratch/stefan/7775246/working/building/REAL300004918645 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918645 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918645/0 /scratch/stefan/7775246/working/building/REAL300004918645 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/649 `/scratch/stefan/7775246/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918645 none CC#CCC(NC(=O)CSC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 88, 88, 21, 88, 5, 1, 1, 1, 1, 1, 1, 1, 1, 123, 156, 156, 201, 201, 201, 201, 201, 123, 88, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 932 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918645 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918645 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918645/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918645 Building REAL300004918646 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918646' /scratch/stefan/7775246/working/building/REAL300004918646 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918646 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918646/0 /scratch/stefan/7775246/working/building/REAL300004918646 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/650 `/scratch/stefan/7775246/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004918646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918646 none CC#CCC(NC(=O)C1=CC=C(OCCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 18, 30, 32, 1, 1, 9, 11, 1, 8, 10, 10, 21, 21, 21, 21, 21, 8, 5, 1, 1, 18, 18, 32, 32, 32, 32, 32, 32, 32, 11, 11, 12, 12, 12, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 48, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918646 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918646 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918646/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918646 Building REAL300004918647 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918647' /scratch/stefan/7775246/working/building/REAL300004918647 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918647 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918647/0 /scratch/stefan/7775246/working/building/REAL300004918647 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/651 `/scratch/stefan/7775246/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004918647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918647 none CC#CCC(NC(=O)C=CC1=CC=C(OCCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 23, 20, 20, 5, 20, 5, 1, 1, 1, 1, 1, 1, 10, 24, 40, 42, 1, 1, 9, 11, 1, 23, 23, 23, 26, 26, 26, 26, 26, 23, 20, 5, 5, 1, 1, 24, 24, 42, 42, 42, 42, 42, 42, 42, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 19, 20, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918647 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918647 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918647/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918647 Building REAL300004918648 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918648' /scratch/stefan/7775246/working/building/REAL300004918648 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918648 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918648/0 /scratch/stefan/7775246/working/building/REAL300004918648 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/652 `/scratch/stefan/7775246/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=NC2=CC=CC=C2S1)C(=O)[O-]) `REAL300004918648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918648 none CC#CCC(NC(=O)C=CC1=NC2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 101, 52, 52, 12, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 120, 120, 161, 161, 161, 161, 159, 101, 55, 12, 12, 1, 1, 1, 1] 161 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918648 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918648 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918648/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918648 Building REAL300004918649 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918649' /scratch/stefan/7775246/working/building/REAL300004918649 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918649 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918649/0 /scratch/stefan/7775246/working/building/REAL300004918649 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/653 `/scratch/stefan/7775246/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=CC=C2C(C)CC)C1)C(=O)[O-]) `REAL300004918649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918649 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=CC=C2C(C)CC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 6, 8, 8, 12, 1, 34, 52, 52, 83, 83, 83, 83, 83, 34, 11, 1, 1, 1, 6, 6, 5, 6, 8, 8, 8, 8, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 50, 51, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 449 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918649 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=CC=C2C(C)CC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 88, 36, 36, 6, 36, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 6, 88, 129, 129, 180, 180, 180, 180, 180, 88, 36, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 6, 6] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 919 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918649 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918649 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918649/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918649 Building REAL300004918650 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918650' /scratch/stefan/7775246/working/building/REAL300004918650 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918650 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918650/0 /scratch/stefan/7775246/working/building/REAL300004918650 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/654 `/scratch/stefan/7775246/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC)=C1OC(F)F)C(=O)[O-]) `REAL300004918650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918650 none CC#CCC(NC(=O)C1=CC=CC(OC)=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 9, 9, 7, 7, 7, 8, 8, 8, 8, 8, 7, 6, 1, 1, 1, 3, 3, 3, 9] 11 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918650 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918650 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918650/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918650 Building REAL300004918651 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918651' /scratch/stefan/7775246/working/building/REAL300004918651 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918651 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918651/0 /scratch/stefan/7775246/working/building/REAL300004918651 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/655 `/scratch/stefan/7775246/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)CC1=CC=CC2=CC=CC=C21)C(=O)[O-]) `REAL300004918651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918651 none CC#CCC(NC(=O)CNC(=O)CC1=CC=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 182, 134, 134, 51, 139, 23, 23, 4, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 182, 186, 186, 201, 201, 201, 201, 201, 182, 139, 51, 51, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 854 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918651 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918651 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918651/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918651 Building REAL300004918652 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918652' /scratch/stefan/7775246/working/building/REAL300004918652 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918652 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918652/0 /scratch/stefan/7775246/working/building/REAL300004918652 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/656 `/scratch/stefan/7775246/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918652 none CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 46, 24, 24, 9, 24, 5, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 46, 52, 52, 65, 65, 65, 65, 65, 46, 24, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1] 65 rigid atoms, others: [35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918652 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918652 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918652/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918652 Building REAL300004918653 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918653' /scratch/stefan/7775246/working/building/REAL300004918653 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918653 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918653/0 /scratch/stefan/7775246/working/building/REAL300004918653 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/657 `/scratch/stefan/7775246/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC(=O)C=CC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004918653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918653 none CC#CCC(NC(=O)C(C)NC(=O)C=CC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 151, 96, 96, 30, 96, 14, 30, 14, 3, 14, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 151, 153, 153, 199, 199, 199, 199, 199, 151, 96, 30, 30, 30, 30, 14, 3, 3, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [40, 41, 46, 45, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 871 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918653 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918653 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918653/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918653 Building REAL300004918654 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918654' /scratch/stefan/7775246/working/building/REAL300004918654 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918654 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918654/0 /scratch/stefan/7775246/working/building/REAL300004918654 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/658 `/scratch/stefan/7775246/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004918654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918654 none CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 82, 41, 41, 7, 41, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 82, 126, 126, 158, 158, 158, 158, 158, 82, 41, 7, 7, 2, 2, 2, 3, 3, 1, 3, 3, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 827 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918654 none CC#CCC(NC(=O)C=CC1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 71, 71, 13, 71, 13, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 127, 152, 152, 201, 201, 201, 201, 201, 127, 71, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [38, 39, 40, 41, 42, 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, 43, 44, 45]) total number of confs: 925 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918654 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918654 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918654/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918654 Building REAL300004918655 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918655' /scratch/stefan/7775246/working/building/REAL300004918655 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918655 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918655/0 /scratch/stefan/7775246/working/building/REAL300004918655 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/659 `/scratch/stefan/7775246/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004918655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918655 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 56, 12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 56, 83, 83, 146, 146, 146, 146, 146, 56, 12, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2] 181 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 694 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918655 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 93, 25, 25, 3, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 93, 125, 125, 181, 181, 181, 181, 181, 93, 25, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3] 181 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41]) total number of confs: 840 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918655 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918655 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918655/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918655 Building REAL300004918656 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918656' /scratch/stefan/7775246/working/building/REAL300004918656 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918656 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918656/0 /scratch/stefan/7775246/working/building/REAL300004918656 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/660 `/scratch/stefan/7775246/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)N(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004918656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918656 none CC#CCC(NC(=O)C1=C(Cl)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 29, 47, 47, 105, 105, 105, 105, 105, 29, 6, 6, 6, 1, 6, 6, 2, 2, 2] 157 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918656 none CC#CCC(NC(=O)C1=C(Cl)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 79, 27, 27, 6, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 79, 108, 108, 157, 157, 157, 157, 157, 79, 27, 1, 1, 1, 1, 1, 6, 6, 6] 157 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918656 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918656 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918656/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918656 Building REAL300004918657 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918657' /scratch/stefan/7775246/working/building/REAL300004918657 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918657 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918657/0 /scratch/stefan/7775246/working/building/REAL300004918657 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/661 `/scratch/stefan/7775246/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCCC)C(OC)=C1)C(=O)[O-]) `REAL300004918657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918657 none CC#CCC(NC(=O)C=CC1=CC=C(OCCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 29, 25, 25, 5, 25, 5, 1, 1, 1, 1, 1, 1, 10, 28, 50, 1, 1, 3, 1, 29, 29, 29, 47, 47, 47, 47, 47, 29, 25, 5, 5, 1, 1, 28, 28, 53, 53, 53, 53, 53, 4, 4, 4, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 18, 19, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 412 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918657 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918657 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918657/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918657 Building REAL300004918658 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918658' /scratch/stefan/7775246/working/building/REAL300004918658 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918658 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918658/0 /scratch/stefan/7775246/working/building/REAL300004918658 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/662 `/scratch/stefan/7775246/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918658 none CC#CCC(NC(=O)CCC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 101, 53, 53, 12, 53, 8, 1, 1, 1, 1, 1, 1, 1, 1, 101, 136, 136, 201, 201, 201, 201, 201, 101, 53, 12, 12, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 978 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918658 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918658 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918658/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918658 Building REAL300004918659 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918659' /scratch/stefan/7775246/working/building/REAL300004918659 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918659 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918659/0 /scratch/stefan/7775246/working/building/REAL300004918659 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/663 `/scratch/stefan/7775246/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-]) `REAL300004918659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918659 none CC#CCC(NC(=O)C1=C(Cl)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 15, 15, 11, 15, 15, 15, 1, 1, 1, 15, 21, 21, 26, 26, 26, 26, 26, 15, 6, 6, 6, 15, 15, 15, 15, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918659 none CC#CCC(NC(=O)C1=C(Cl)N(CC2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 56, 56, 15, 56, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 120, 154, 154, 201, 201, 201, 201, 201, 120, 56, 6, 6, 1, 1, 1, 1, 15, 15, 15] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 984 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918659 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918659 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918659/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918659 Building REAL300004918660 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918660' /scratch/stefan/7775246/working/building/REAL300004918660 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918660 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918660/0 /scratch/stefan/7775246/working/building/REAL300004918660 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/664 `/scratch/stefan/7775246/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(N=C3CCCN3C2=O)S1)C(=O)[O-]) `REAL300004918660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918660 none CC#CCC(NC(=O)C1=C(C)C2=C(N=C3CCCN3C2=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 42, 42, 58, 58, 58, 58, 58, 32, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918660 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918660 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918660/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918660 Building REAL300004918661 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918661' /scratch/stefan/7775246/working/building/REAL300004918661 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918661 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918661/0 /scratch/stefan/7775246/working/building/REAL300004918661 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/665 `/scratch/stefan/7775246/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(OC)C=C2N1)C(=O)[O-]) `REAL300004918661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918661 none CC#CCC(NC(=O)C1=CC2=CC=C(OC)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 43, 65, 65, 107, 107, 107, 107, 107, 43, 12, 1, 1, 1, 2, 2, 2, 1, 1] 128 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 34, 15, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918661 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918661 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918661/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918661 Building REAL300004918662 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918662' /scratch/stefan/7775246/working/building/REAL300004918662 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918662 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918662/0 /scratch/stefan/7775246/working/building/REAL300004918662 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/666 `/scratch/stefan/7775246/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC=CN=C1C(=O)NCC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918662 none CC#CCC(NC(=O)C1=NC=CN=C1C(=O)NCC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 38, 44, 44, 38, 44, 44, 44, 23, 33, 33, 53, 53, 53, 53, 53, 23, 9, 1, 1, 10, 38, 38, 44, 44, 44, 44] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918662 none CC#CCC(NC(=O)C1=NC=CN=C1C(=O)NCC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 84, 84, 44, 84, 44, 44, 44, 44, 44, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 135, 168, 168, 201, 201, 201, 201, 201, 135, 84, 44, 44, 12, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 928 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918662 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918662 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918662/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918662 Building REAL300004918663 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918663' /scratch/stefan/7775246/working/building/REAL300004918663 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918663 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918663/0 /scratch/stefan/7775246/working/building/REAL300004918663 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/667 `/scratch/stefan/7775246/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918663 none CC#CCC(NC(=O)CCCC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 92, 40, 40, 8, 40, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 140, 140, 201, 201, 201, 201, 201, 92, 40, 8, 8, 4, 4, 3, 3, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1046 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918663 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918663 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918663/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918663 Building REAL300004918664 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918664' /scratch/stefan/7775246/working/building/REAL300004918664 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918664 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918664/0 /scratch/stefan/7775246/working/building/REAL300004918664 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/668 `/scratch/stefan/7775246/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(C)=C2)CCCCC1)C(=O)[O-]) `REAL300004918664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918664 none CC#CCC(NC(=O)C1(C2=CC=CC(C)=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 18, 5, 5, 1, 5, 1, 1, 13, 13, 1, 13, 13, 13, 1, 1, 1, 1, 1, 18, 31, 31, 49, 49, 49, 49, 49, 18, 5, 13, 13, 1, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 6, 39, 8, 9, 42, 43, 45, 46, 44, 16, 17, 18, 19, 20, 41, 40, 47] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918664 none CC#CCC(NC(=O)C1(C2=CC=CC(C)=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 99, 35, 35, 13, 35, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 99, 135, 135, 201, 201, 201, 201, 201, 99, 35, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 37, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 998 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918664 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918664 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918664/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918664 Building REAL300004918665 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918665' /scratch/stefan/7775246/working/building/REAL300004918665 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918665 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918665/0 /scratch/stefan/7775246/working/building/REAL300004918665 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/669 `/scratch/stefan/7775246/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918665 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 42, 42, 7, 42, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 98, 131, 131, 201, 201, 201, 201, 201, 98, 42, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 929 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918665 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918665 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918665/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918665 Building REAL300004918666 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918666' /scratch/stefan/7775246/working/building/REAL300004918666 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918666 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918666/0 /scratch/stefan/7775246/working/building/REAL300004918666 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/670 `/scratch/stefan/7775246/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C=C1Br)C(=O)[O-]) `REAL300004918666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918666 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 28, 7, 7, 1, 7, 1, 1, 1, 1, 8, 8, 2, 8, 8, 9, 1, 1, 1, 28, 47, 47, 86, 86, 86, 86, 86, 28, 7, 8, 8, 7, 8, 1] 196 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918666 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 110, 39, 39, 8, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 110, 146, 146, 196, 196, 196, 196, 196, 110, 39, 1, 1, 1, 1, 8] 196 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 939 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918666 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918666 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918666/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918666 Building REAL300004918667 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918667' /scratch/stefan/7775246/working/building/REAL300004918667 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918667 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918667/0 /scratch/stefan/7775246/working/building/REAL300004918667 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/671 `/scratch/stefan/7775246/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CS(=O)(=O)C1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918667 none CC#CCC(NC(=O)CS(=O)(=O)C1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 65, 65, 18, 65, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 119, 159, 159, 201, 201, 201, 201, 201, 119, 65, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1022 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918667 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918667 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918667/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918667 Building REAL300004918668 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918668' /scratch/stefan/7775246/working/building/REAL300004918668 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918668 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918668/0 /scratch/stefan/7775246/working/building/REAL300004918668 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/672 `/scratch/stefan/7775246/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=C(OC)C(OC)=C2)S1)C(=O)[O-]) `REAL300004918668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918668 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=C(OC)C(OC)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 4, 4, 12, 4, 1, 21, 36, 36, 54, 54, 54, 54, 54, 21, 8, 2, 2, 2, 4, 4, 13, 13, 13, 12, 13, 13, 4] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918668 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=C(OC)C(OC)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 61, 26, 26, 4, 26, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 1, 4, 61, 99, 99, 128, 128, 128, 128, 128, 61, 26, 5, 5, 5, 1, 1, 4, 4, 4, 3, 4, 4, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918668 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918668 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918668/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918668 Building REAL300004918669 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918669' /scratch/stefan/7775246/working/building/REAL300004918669 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918669 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918669/0 /scratch/stefan/7775246/working/building/REAL300004918669 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/673 `/scratch/stefan/7775246/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(N2C=CC=N2)C=C1)C(=O)[O-]) `REAL300004918669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918669 none CC#CCC(NC(=O)CC1=CC=C(N2C=CC=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 35, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 35, 56, 56, 111, 111, 111, 111, 111, 35, 10, 4, 4, 1, 1, 6, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918669 none CC#CCC(NC(=O)CC1=CC=C(N2C=CC=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 76, 27, 27, 11, 26, 2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 76, 115, 115, 201, 201, 201, 201, 201, 76, 27, 12, 11, 6, 6, 1, 1, 1, 6, 6] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 979 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918669 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918669 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918669/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918669 Building REAL300004918670 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918670' /scratch/stefan/7775246/working/building/REAL300004918670 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918670 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918670/0 /scratch/stefan/7775246/working/building/REAL300004918670 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/674 `/scratch/stefan/7775246/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(N2N=C(C)C=C2C)C=C1)C(=O)[O-]) `REAL300004918670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918670 none CC#CCC(NC(=O)CC1=CC=C(N2N=C(C)C=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 32, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 32, 47, 47, 80, 80, 80, 80, 80, 32, 9, 4, 4, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 44, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 401 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918670 none CC#CCC(NC(=O)CC1=CC=C(N2N=C(C)C=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 40, 19, 40, 4, 3, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 104, 141, 141, 201, 201, 201, 201, 201, 104, 40, 19, 19, 9, 9, 2, 2, 2, 1, 2, 2, 2, 9, 9] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 1030 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918670 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918670 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918670/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918670 Building REAL300004918671 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918671' /scratch/stefan/7775246/working/building/REAL300004918671 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918671 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918671/0 /scratch/stefan/7775246/working/building/REAL300004918671 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/675 `/scratch/stefan/7775246/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C([N+](=O)[O-])C=C2)C=C1)C(=O)[O-]) `REAL300004918671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918671 none CC#CCC(NC(=O)C1=NN(C2=CC=C([N+](=O)[O-])C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 32, 11, 11, 1, 11, 1, 1, 1, 1, 4, 4, 1, 3, 4, 4, 4, 4, 1, 1, 32, 47, 47, 65, 65, 65, 65, 65, 32, 11, 4, 4, 4, 4, 1, 1] 74 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918671 none CC#CCC(NC(=O)C1=NN(C2=CC=C([N+](=O)[O-])C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 47, 23, 23, 4, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 47, 57, 57, 74, 74, 74, 74, 74, 47, 23, 1, 1, 1, 1, 4, 4] 74 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918671 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918671 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918671/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918671 Building REAL300004918672 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918672' /scratch/stefan/7775246/working/building/REAL300004918672 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918672 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918672/0 /scratch/stefan/7775246/working/building/REAL300004918672 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/676 `/scratch/stefan/7775246/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(C)O2)=NN1)C(=O)[O-]) `REAL300004918672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918672 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)O2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 40, 12, 12, 1, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 40, 59, 59, 101, 101, 101, 101, 101, 40, 13, 1, 12, 12, 13, 13, 13, 1] 188 rigid atoms, others: [35, 6, 8, 9, 10, 11, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918672 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)O2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 124, 67, 67, 12, 68, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 124, 154, 154, 188, 188, 188, 188, 188, 124, 68, 12, 1, 1, 2, 2, 2, 12] 188 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 870 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918672 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918672 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918672/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918672 Building REAL300004918673 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918673' /scratch/stefan/7775246/working/building/REAL300004918673 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918673 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918673/0 /scratch/stefan/7775246/working/building/REAL300004918673 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/677 `/scratch/stefan/7775246/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2OCC)=NN1)C(=O)[O-]) `REAL300004918673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918673 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2OCC)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 15, 5, 5, 1, 5, 1, 1, 1, 1, 11, 11, 3, 11, 11, 11, 29, 65, 1, 1, 15, 22, 22, 38, 38, 38, 38, 38, 15, 6, 1, 11, 11, 11, 11, 65, 65, 65, 65, 65, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918673 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2OCC)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 61, 31, 31, 11, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 11, 11, 61, 89, 89, 126, 126, 126, 126, 126, 61, 31, 11, 1, 1, 1, 1, 24, 24, 24, 24, 24, 11] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918673 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918673 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918673/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918673 Building REAL300004918674 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918674' /scratch/stefan/7775246/working/building/REAL300004918674 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918674 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918674/0 /scratch/stefan/7775246/working/building/REAL300004918674 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/678 `/scratch/stefan/7775246/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C(C)(C)C)C(C2CC2)=C1)C(=O)[O-]) `REAL300004918674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918674 none CC#CCC(NC(=O)C1=NN(C(C)(C)C)C(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 25, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 25, 39, 39, 73, 73, 73, 73, 73, 25, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 1] 110 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 44] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 361 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918674 none CC#CCC(NC(=O)C1=NN(C(C)(C)C)C(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 55, 30, 30, 6, 30, 6, 6, 6, 6, 7, 7, 7, 1, 1, 1, 1, 6, 55, 74, 74, 110, 110, 110, 110, 110, 55, 30, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6] 110 rigid atoms, others: [39, 40, 41, 42, 43, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 505 number of broken/clashed sets: 110 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918674 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918674 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918674/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918674 Building REAL300004918675 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918675' /scratch/stefan/7775246/working/building/REAL300004918675 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918675 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918675/0 /scratch/stefan/7775246/working/building/REAL300004918675 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/679 `/scratch/stefan/7775246/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCC2)=C(C)O1)C(=O)[O-]) `REAL300004918675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918675 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCC2)=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 28, 10, 10, 1, 10, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 1, 1, 1, 28, 41, 41, 83, 83, 83, 83, 83, 28, 11, 1, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918675 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCC2)=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 69, 69, 17, 69, 17, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 17, 17, 17, 119, 149, 149, 201, 201, 201, 201, 201, 119, 69, 17, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 920 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918675 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918675 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918675/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918675 Building REAL300004918676 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918676' /scratch/stefan/7775246/working/building/REAL300004918676 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918676 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918676/0 /scratch/stefan/7775246/working/building/REAL300004918676 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/680 `/scratch/stefan/7775246/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC(OC)=C1)N1N=NN=C1C)C(=O)[O-]) `REAL300004918676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918676 none CC#CCC(NC(=O)C(CC1=CC=CC(OC)=C1)N1N=NN=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 73, 31, 31, 9, 31, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 9, 15, 15, 15, 15, 15, 73, 81, 81, 132, 132, 132, 132, 132, 73, 31, 9, 3, 3, 1, 1, 1, 3, 3, 3, 1, 15, 15, 15] 146 rigid atoms, others: [43, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 44, 45, 46]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918676 none CC#CCC(NC(=O)C(CC1=CC=CC(OC)=C1)N1N=NN=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 32, 17, 17, 5, 17, 1, 5, 9, 15, 15, 15, 15, 15, 25, 15, 1, 1, 1, 1, 1, 1, 32, 34, 34, 72, 72, 72, 72, 72, 32, 17, 5, 9, 9, 15, 15, 15, 25, 25, 25, 15, 2, 2, 2] 146 rigid atoms, others: [8, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918676 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918676 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918676/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918676 Building REAL300004918677 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918677' /scratch/stefan/7775246/working/building/REAL300004918677 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918677 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918677/0 /scratch/stefan/7775246/working/building/REAL300004918677 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/681 `/scratch/stefan/7775246/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=C(F)C=C1)N1N=NN=C1C)C(=O)[O-]) `REAL300004918677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918677 none CC#CCC(NC(=O)C(CC1=CC=C(F)C=C1)N1N=NN=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 81, 31, 31, 6, 31, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 17, 81, 113, 113, 147, 147, 147, 147, 147, 81, 31, 6, 3, 3, 1, 1, 1, 1, 17, 17, 17] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 766 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918677 none CC#CCC(NC(=O)C(CC1=CC=C(F)C=C1)N1N=NN=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 81, 33, 33, 6, 33, 1, 6, 16, 17, 17, 16, 16, 17, 17, 1, 1, 1, 1, 1, 1, 81, 111, 111, 160, 160, 160, 160, 160, 81, 33, 6, 16, 16, 17, 17, 17, 17, 2, 2, 2] 201 rigid atoms, others: [8, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 817 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918677 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918677 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918677/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918677 Building REAL300004918678 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918678' /scratch/stefan/7775246/working/building/REAL300004918678 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918678 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918678/0 /scratch/stefan/7775246/working/building/REAL300004918678 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/682 `/scratch/stefan/7775246/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC(F)=C1)N1N=NN=C1C)C(=O)[O-]) `REAL300004918678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918678 none CC#CCC(NC(=O)C(CC1=CC=CC(F)=C1)N1N=NN=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 100, 46, 46, 9, 46, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 100, 134, 134, 170, 170, 170, 170, 170, 100, 46, 9, 3, 3, 1, 1, 1, 1, 21, 21, 21] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 854 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918678 none CC#CCC(NC(=O)C(CC1=CC=CC(F)=C1)N1N=NN=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 55, 26, 26, 6, 26, 1, 6, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 55, 81, 81, 99, 99, 99, 99, 99, 55, 26, 6, 13, 13, 21, 21, 21, 21, 2, 2, 2] 201 rigid atoms, others: [8, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 562 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918678 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918678 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918678/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918678 Building REAL300004918679 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918679' /scratch/stefan/7775246/working/building/REAL300004918679 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918679 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918679/0 /scratch/stefan/7775246/working/building/REAL300004918679 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/683 `/scratch/stefan/7775246/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC)N(C(C)(C)C)N=C1)C(=O)[O-]) `REAL300004918679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918679 none CC#CCC(NC(=O)C1=C(CC)N(C(C)(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 11, 5, 5, 1, 5, 1, 1, 1, 3, 1, 1, 2, 2, 2, 1, 1, 11, 16, 16, 23, 23, 23, 23, 23, 11, 5, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 23 rigid atoms, others: [6, 8, 9, 10, 43, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 11, 14, 15, 16, 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: 124 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918679 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918679 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918679/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918679 Building REAL300004918680 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918680' /scratch/stefan/7775246/working/building/REAL300004918680 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918680 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918680/0 /scratch/stefan/7775246/working/building/REAL300004918680 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/684 `/scratch/stefan/7775246/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C=C(Br)O1)C(=O)[O-]) `REAL300004918680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918680 none CC#CCC(NC(=O)C1=C(C)C=C(Br)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'Br', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 17, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 34, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 34, 46, 46, 66, 66, 66, 66, 66, 34, 13, 2, 2, 2, 1] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 318 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918680 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918680 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918680/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918680 Building REAL300004918681 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918681' /scratch/stefan/7775246/working/building/REAL300004918681 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918681 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918681/0 /scratch/stefan/7775246/working/building/REAL300004918681 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/685 `/scratch/stefan/7775246/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2NC(=O)C3=CC=CC=C3N2N=C1)C(=O)[O-]) `REAL300004918681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918681 none CC#CCC(NC(=O)C1=C2NC(=O)C3=CC=CC=C3N2N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 39, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 73, 73, 73, 73, 73, 39, 11, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918681 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918681 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918681/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918681 Building REAL300004918682 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918682' /scratch/stefan/7775246/working/building/REAL300004918682 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918682 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918682/0 /scratch/stefan/7775246/working/building/REAL300004918682 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/686 `/scratch/stefan/7775246/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2=NC=CC=N2)=NO1)C(=O)[O-]) `REAL300004918682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918682 none CC#CCC(NC(=O)CCC1=NC(C2=NC=CC=N2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 56, 38, 38, 13, 38, 8, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 56, 79, 79, 83, 83, 83, 83, 83, 56, 38, 13, 13, 8, 8, 7, 2, 7] 88 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918682 none CC#CCC(NC(=O)CCC1=NC(C2=NC=CC=N2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 62, 44, 44, 18, 44, 15, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 62, 86, 86, 88, 88, 88, 88, 88, 62, 44, 18, 18, 15, 15, 1, 1, 1] 88 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918682 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918682 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918682/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918682 Building REAL300004918683 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918683' /scratch/stefan/7775246/working/building/REAL300004918683 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918683 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918683/0 /scratch/stefan/7775246/working/building/REAL300004918683 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/687 `/scratch/stefan/7775246/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(OC)C=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004918683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918683 none CC#CCC(NC(=O)C1=C(OC)C=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 33, 12, 12, 1, 12, 1, 1, 1, 4, 1, 1, 1, 7, 7, 1, 7, 7, 1, 33, 53, 53, 89, 89, 89, 89, 89, 33, 12, 4, 4, 4, 1, 7, 7, 1, 7, 7] 201 rigid atoms, others: [34, 6, 8, 9, 10, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 7, 11, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918683 none CC#CCC(NC(=O)C1=C(OC)C=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 111, 56, 56, 7, 56, 7, 7, 7, 19, 7, 1, 1, 1, 1, 1, 1, 1, 7, 111, 156, 156, 186, 186, 186, 186, 186, 111, 56, 19, 19, 19, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 955 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918683 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918683 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918683/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918683 Building REAL300004918684 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918684' /scratch/stefan/7775246/working/building/REAL300004918684 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918684 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918684/0 /scratch/stefan/7775246/working/building/REAL300004918684 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/688 `/scratch/stefan/7775246/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(OCC)C=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004918684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918684 none CC#CCC(NC(=O)C1=C(OCC)C=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 22, 8, 8, 1, 8, 1, 1, 1, 9, 29, 1, 1, 1, 6, 6, 1, 6, 6, 1, 22, 36, 36, 55, 55, 55, 55, 55, 22, 8, 29, 29, 30, 30, 30, 1, 6, 6, 1, 6, 6] 201 rigid atoms, others: [37, 6, 8, 9, 10, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918684 none CC#CCC(NC(=O)C1=C(OCC)C=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 76, 36, 36, 6, 36, 6, 6, 6, 33, 89, 6, 1, 1, 1, 1, 1, 1, 1, 6, 76, 116, 116, 143, 143, 143, 143, 143, 76, 36, 89, 89, 89, 89, 89, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 995 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918684 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918684 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918684/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918684 Building REAL300004918685 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918685' /scratch/stefan/7775246/working/building/REAL300004918685 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918685 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918685/0 /scratch/stefan/7775246/working/building/REAL300004918685 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/689 `/scratch/stefan/7775246/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CN1CC)C(=O)[O-]) `REAL300004918685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918685 none CC#CCC(NC(=O)C1=CC(Br)=CN1CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 47, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 47, 72, 72, 121, 121, 121, 121, 121, 47, 12, 1, 1, 6, 6, 6, 6, 6] 181 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 578 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918685 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918685 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918685/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918685 Building REAL300004918686 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918686' /scratch/stefan/7775246/working/building/REAL300004918686 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918686 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918686/0 /scratch/stefan/7775246/working/building/REAL300004918686 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/690 `/scratch/stefan/7775246/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CN1C(C)C)C(=O)[O-]) `REAL300004918686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918686 none CC#CCC(NC(=O)C1=CC(Br)=CN1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 78, 78, 124, 124, 124, 124, 124, 49, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7] 159 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 627 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918686 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918686 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918686/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918686 Building REAL300004918687 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918687' /scratch/stefan/7775246/working/building/REAL300004918687 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918687 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918687/0 /scratch/stefan/7775246/working/building/REAL300004918687 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/691 `/scratch/stefan/7775246/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC[NH+](CC2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004918687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918687 none CC#CCC(NC(=O)C1CC[NH+](CC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 47, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 10, 10, 8, 10, 10, 1, 1, 47, 69, 69, 105, 105, 105, 105, 105, 47, 13, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 46, 44, 20, 21, 45, 47] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918687 none CC#CCC(NC(=O)C1CC[NH+](CC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 56, 56, 10, 56, 10, 10, 10, 3, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 119, 151, 151, 201, 201, 201, 201, 201, 119, 56, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47]) total number of confs: 914 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918687 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918687 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918687/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918687 Building REAL300004918688 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918688' /scratch/stefan/7775246/working/building/REAL300004918688 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918688 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918688/0 /scratch/stefan/7775246/working/building/REAL300004918688 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/692 `/scratch/stefan/7775246/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CCC)C(C(C)=O)=C(C)N1)C(=O)[O-]) `REAL300004918688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918688 none CC#CCC(NC(=O)C1=C(CCC)C(C(C)=O)=C(C)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 5, 11, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 25, 9, 10, 1, 10, 1, 1, 1, 2, 5, 1, 1, 11, 11, 1, 1, 1, 25, 39, 39, 61, 61, 61, 61, 61, 25, 10, 2, 2, 5, 5, 6, 6, 6, 11, 11, 11, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 43, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 355 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918688 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918688 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918688/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918688 Building REAL300004918689 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918689' /scratch/stefan/7775246/working/building/REAL300004918689 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918689 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918689/0 /scratch/stefan/7775246/working/building/REAL300004918689 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/693 `/scratch/stefan/7775246/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CO2)=C1)C(=O)[O-]) `REAL300004918689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918689 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 1, 17, 28, 28, 53, 53, 53, 53, 53, 17, 5, 1, 1, 1, 9, 16, 16, 16, 1] 201 rigid atoms, others: [32, 33, 34, 6, 39, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918689 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 48, 48, 16, 48, 16, 16, 16, 16, 5, 4, 1, 4, 1, 1, 1, 1, 1, 16, 103, 132, 132, 201, 201, 201, 201, 201, 103, 48, 16, 16, 16, 5, 1, 1, 1, 16] 201 rigid atoms, others: [36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918689 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918689 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918689/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918689 Building REAL300004918690 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918690' /scratch/stefan/7775246/working/building/REAL300004918690 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918690 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918690/0 /scratch/stefan/7775246/working/building/REAL300004918690 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/694 `/scratch/stefan/7775246/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC2CC2)C=C1)C(=O)[O-]) `REAL300004918690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918690 none CC#CCC(NC(=O)C1=CC=C(OCC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 13, 40, 40, 1, 1, 8, 13, 13, 25, 25, 25, 25, 25, 8, 3, 1, 1, 13, 13, 40, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918690 none CC#CCC(NC(=O)C1=CC=C(OCC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 107, 61, 61, 40, 61, 37, 40, 40, 23, 9, 1, 1, 1, 1, 40, 40, 107, 137, 137, 201, 201, 201, 201, 201, 107, 61, 40, 40, 9, 9, 1, 1, 1, 1, 1, 40, 40] 201 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 928 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918690 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918690 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918690/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918690 Building REAL300004918691 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918691' /scratch/stefan/7775246/working/building/REAL300004918691 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918691 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918691/0 /scratch/stefan/7775246/working/building/REAL300004918691 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/695 `/scratch/stefan/7775246/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC1=CC=CC=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918691 none CC#CCC(NC(=O)CNC1=CC=CC=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 68, 68, 18, 68, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 118, 155, 155, 201, 201, 201, 201, 201, 118, 68, 18, 18, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 989 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918691 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918691 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918691/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918691 Building REAL300004918692 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918692' /scratch/stefan/7775246/working/building/REAL300004918692 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918692 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918692/0 /scratch/stefan/7775246/working/building/REAL300004918692 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/696 `/scratch/stefan/7775246/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004918692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918692 none CC#CCC(NC(=O)COC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 125, 85, 85, 24, 85, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 159, 159, 201, 201, 201, 201, 201, 125, 85, 24, 24, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 980 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918692 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918692 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918692/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918692 Building REAL300004918693 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918693' /scratch/stefan/7775246/working/building/REAL300004918693 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918693 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918693/0 /scratch/stefan/7775246/working/building/REAL300004918693 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/697 `/scratch/stefan/7775246/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1Br)C(=O)[O-]) `REAL300004918693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918693 none CC#CCC(NC(=O)C1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 22, 32, 32, 56, 56, 56, 56, 56, 22, 7, 1, 1, 1, 1] 56 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 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/7775246/working/building/REAL300004918693 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918693 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918693/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918693 Building REAL300004918694 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918694' /scratch/stefan/7775246/working/building/REAL300004918694 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918694 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918694/0 /scratch/stefan/7775246/working/building/REAL300004918694 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/698 `/scratch/stefan/7775246/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918694 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 26, 26, 26, 26, 26, 10, 4, 1, 1, 1, 1] 26 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918694 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918694 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918694/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918694 Building REAL300004918695 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918695' /scratch/stefan/7775246/working/building/REAL300004918695 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918695 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918695/0 /scratch/stefan/7775246/working/building/REAL300004918695 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/699 `/scratch/stefan/7775246/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC(C)=CC=C1C)C(=O)[O-]) `REAL300004918695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918695 none CC#CCC(NC(=O)CSC1=CC(C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 90, 90, 25, 90, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 158, 158, 201, 201, 201, 201, 201, 125, 90, 25, 25, 1, 2, 2, 2, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38]) total number of confs: 994 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918695 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918695 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918695/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918695 Building REAL300004918696 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918696' /scratch/stefan/7775246/working/building/REAL300004918696 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918696 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918696/0 /scratch/stefan/7775246/working/building/REAL300004918696 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/700 `/scratch/stefan/7775246/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC(C)=C(Br)C=C1C)C(=O)[O-]) `REAL300004918696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918696 none CC#CCC(NC(=O)CSC1=CC(C)=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 5, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 84, 84, 26, 84, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 155, 155, 201, 201, 201, 201, 201, 122, 84, 26, 26, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38]) total number of confs: 1003 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918696 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918696 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918696/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918696 Building REAL300004918697 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918697' /scratch/stefan/7775246/working/building/REAL300004918697 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918697 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918697/0 /scratch/stefan/7775246/working/building/REAL300004918697 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/701 `/scratch/stefan/7775246/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC=C1)C(=O)[O-]) `REAL300004918697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918697 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 8, 14, 14, 39, 63, 63, 111, 111, 111, 111, 111, 39, 12, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14] 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, 40]) total number of confs: 587 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918697 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 76, 76, 14, 76, 14, 14, 9, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 136, 165, 165, 201, 201, 201, 201, 201, 136, 76, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 936 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918697 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918697 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918697/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918697 Building REAL300004918698 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918698' /scratch/stefan/7775246/working/building/REAL300004918698 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918698 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918698/0 /scratch/stefan/7775246/working/building/REAL300004918698 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/702 `/scratch/stefan/7775246/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918698 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 1, 9, 15, 15, 32, 32, 32, 32, 32, 9, 3, 1, 1, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [32, 38, 6, 39, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918698 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 91, 35, 35, 19, 35, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 91, 118, 118, 201, 201, 201, 201, 201, 91, 35, 19, 19, 1, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 913 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918698 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918698 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918698/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918698 Building REAL300004918699 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918699' /scratch/stefan/7775246/working/building/REAL300004918699 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918699 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918699/0 /scratch/stefan/7775246/working/building/REAL300004918699 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/703 `/scratch/stefan/7775246/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918699 none CC#CCC(NC(=O)C1=CC=C(Cl)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 19, 25, 25, 39, 39, 39, 39, 39, 19, 6, 1, 1, 1] 39 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918699 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918699 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918699/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918699 Building REAL300004918700 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918700' /scratch/stefan/7775246/working/building/REAL300004918700 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918700 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918700/0 /scratch/stefan/7775246/working/building/REAL300004918700 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/704 `/scratch/stefan/7775246/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(I)C=C1)C(=O)[O-]) `REAL300004918700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918700 none CC#CCC(NC(=O)C1=CC=C(I)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 26, 26, 26, 26, 26, 10, 4, 1, 1, 1, 1] 26 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918700 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918700 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918700/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918700 Building REAL300004918701 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918701' /scratch/stefan/7775246/working/building/REAL300004918701 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918701 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918701/0 /scratch/stefan/7775246/working/building/REAL300004918701 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/705 `/scratch/stefan/7775246/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004918701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918701 none CC#CCC(NC(=O)C=CC1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 50, 20, 20, 4, 21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 63, 63, 85, 85, 85, 85, 85, 50, 21, 4, 4, 1, 1, 1, 1] 85 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 399 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918701 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918701 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918701/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918701 Building REAL300004918702 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918702' /scratch/stefan/7775246/working/building/REAL300004918702 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918702 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918702/0 /scratch/stefan/7775246/working/building/REAL300004918702 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/706 `/scratch/stefan/7775246/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CC3CC(CC(Cl)(C3)C1)C2)C(=O)[O-]) `REAL300004918702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918702 none CC#CCC(NC(=O)C12CC3CC(CC(Cl)(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 16, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 44, 44, 83, 83, 83, 83, 83, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918702 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918702 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918702/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918702 Building REAL300004918703 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918703' /scratch/stefan/7775246/working/building/REAL300004918703 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918703 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918703/0 /scratch/stefan/7775246/working/building/REAL300004918703 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/707 `/scratch/stefan/7775246/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC12CC3CC(CC(Br)(C3)C1)C2)C(=O)[O-]) `REAL300004918703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918703 none CC#CCC(NC(=O)CC12CC3CC(CC(Br)(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'Br', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 17, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 96, 36, 36, 9, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 134, 134, 201, 201, 201, 201, 201, 96, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 981 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918703 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918703 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918703/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918703 Building REAL300004918704 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918704' /scratch/stefan/7775246/working/building/REAL300004918704 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918704 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918704/0 /scratch/stefan/7775246/working/building/REAL300004918704 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/708 `/scratch/stefan/7775246/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918704 none CC#CCC(NC(=O)CCCOC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 94, 94, 37, 94, 27, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 127, 158, 158, 201, 201, 201, 201, 201, 127, 94, 37, 37, 27, 27, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1054 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918704 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918704 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918704/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918704 Building REAL300004918705 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918705' /scratch/stefan/7775246/working/building/REAL300004918705 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918705 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918705/0 /scratch/stefan/7775246/working/building/REAL300004918705 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/709 `/scratch/stefan/7775246/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=CC=C(OCCCCC)C=C1)C(=O)[O-]) `REAL300004918705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918705 none CC#CCC(NC(=O)CCC(=O)C1=CC=C(OCCCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 23, 17, 17, 9, 17, 7, 4, 1, 4, 1, 1, 1, 1, 1, 6, 10, 22, 22, 23, 1, 1, 23, 28, 28, 41, 41, 41, 41, 41, 23, 17, 9, 9, 7, 7, 1, 1, 10, 10, 22, 22, 23, 23, 22, 22, 23, 23, 23, 1, 1] 201 rigid atoms, others: [38, 39, 10, 12, 13, 14, 15, 16, 51, 52, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918705 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918705 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918705/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918705 Building REAL300004918706 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918706' /scratch/stefan/7775246/working/building/REAL300004918706 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918706 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918706/0 /scratch/stefan/7775246/working/building/REAL300004918706 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/710 `/scratch/stefan/7775246/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2NC3=C(CCCC3)C2=C1)C(=O)[O-]) `REAL300004918706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918706 none CC#CCC(NC(=O)C1=CC=C2NC3=C(CCCC3)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 36, 36, 65, 65, 65, 65, 65, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 306 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918706 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918706 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918706/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918706 Building REAL300004918707 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918707' /scratch/stefan/7775246/working/building/REAL300004918707 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918707 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918707/0 /scratch/stefan/7775246/working/building/REAL300004918707 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/711 `/scratch/stefan/7775246/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=CC=C1OC)C(C)C)C(=O)[O-]) `REAL300004918707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918707 none CC#CCC(NC(=O)C(NC(=O)C1=CC=CC=C1OC)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 130, 86, 86, 24, 86, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 3, 24, 63, 65, 130, 162, 162, 191, 191, 191, 191, 191, 130, 86, 24, 12, 1, 1, 1, 1, 4, 4, 4, 65, 65, 65, 65, 65, 65, 65] 201 rigid atoms, others: [35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918707 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918707 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918707/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918707 Building REAL300004918708 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918708' /scratch/stefan/7775246/working/building/REAL300004918708 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918708 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918708/0 /scratch/stefan/7775246/working/building/REAL300004918708 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/712 `/scratch/stefan/7775246/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NS(=O)(=O)C1=CC=C(OC)C=C1)C(C)C)C(=O)[O-]) `REAL300004918708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918708 none CC#CCC(NC(=O)C(NS(=O)(=O)C1=CC=C(OC)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 19, 14, 14, 3, 14, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 1, 1, 3, 7, 7, 19, 19, 19, 34, 34, 34, 34, 34, 19, 14, 3, 3, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7] 36 rigid atoms, others: [36, 37, 41, 10, 13, 14, 15, 16, 17, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44, 45, 46, 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/7775246/working/building/REAL300004918708 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918708 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918708/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918708 Building REAL300004918709 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918709' /scratch/stefan/7775246/working/building/REAL300004918709 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918709 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918709/0 /scratch/stefan/7775246/working/building/REAL300004918709 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/713 `/scratch/stefan/7775246/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC(=O)C1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918709 none CC#CCC(NC(=O)C(C)NC(=O)C1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 59, 59, 14, 59, 5, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 107, 155, 155, 201, 201, 201, 201, 201, 107, 59, 14, 14, 14, 14, 5, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1059 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918709 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918709 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918709/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918709 Building REAL300004918710 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918710' /scratch/stefan/7775246/working/building/REAL300004918710 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918710 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918710/0 /scratch/stefan/7775246/working/building/REAL300004918710 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/714 `/scratch/stefan/7775246/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC(=O)C2=CC=CC=C2N1)C(=O)[O-]) `REAL300004918710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918710 none CC#CCC(NC(=O)CCCC1=NC(=O)C2=CC=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 53, 29, 29, 11, 29, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 56, 56, 71, 71, 71, 71, 71, 53, 29, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1] 71 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918710 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918710 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918710/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918710 Building REAL300004918711 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918711' /scratch/stefan/7775246/working/building/REAL300004918711 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918711 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918711/0 /scratch/stefan/7775246/working/building/REAL300004918711 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/715 `/scratch/stefan/7775246/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)C(C)C)C=C1)C(=O)[O-]) `REAL300004918711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918711 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 26, 1, 1, 9, 17, 17, 43, 43, 43, 43, 43, 9, 3, 1, 1, 27, 27, 27, 26, 27, 27, 27, 27, 27, 27, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918711 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918711 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918711/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918711 Building REAL300004918712 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918712' /scratch/stefan/7775246/working/building/REAL300004918712 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918712 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918712/0 /scratch/stefan/7775246/working/building/REAL300004918712 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/716 `/scratch/stefan/7775246/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=C(C)ON=C1C)C(=O)[O-]) `REAL300004918712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918712 none CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=C(C)ON=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 5, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 33, 22, 22, 15, 22, 15, 15, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 41, 41, 41, 41, 41, 33, 22, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2] 41 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918712 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918712 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918712/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918712 Building REAL300004918713 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918713' /scratch/stefan/7775246/working/building/REAL300004918713 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918713 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918713/0 /scratch/stefan/7775246/working/building/REAL300004918713 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/717 `/scratch/stefan/7775246/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(C2CC2C)O1)C(=O)[O-]) `REAL300004918713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918713 none CC#CCC(NC(=O)CCC1=CC=C(C2CC2C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 81, 53, 53, 14, 52, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 81, 107, 107, 117, 117, 117, 117, 117, 81, 53, 14, 14, 6, 6, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918713 none CC#CCC(NC(=O)CCC1=CC=C(C2CC2C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 123, 123, 52, 123, 36, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 157, 191, 191, 201, 201, 201, 201, 201, 157, 123, 52, 52, 36, 36, 10, 10, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 1001 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918713 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918713 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918713/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918713 Building REAL300004918714 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918714' /scratch/stefan/7775246/working/building/REAL300004918714 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918714 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918714/0 /scratch/stefan/7775246/working/building/REAL300004918714 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/718 `/scratch/stefan/7775246/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CCCC1)C(=O)[O-]) `REAL300004918714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918714 none CC#CCC(NC(=O)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 30, 10, 10, 1, 10, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 30, 44, 44, 71, 71, 71, 71, 71, 30, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 98 rigid atoms, others: [37, 6, 39, 8, 9, 42, 43, 44, 40, 19, 20, 21, 22, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 353 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918714 none CC#CCC(NC(=O)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 58, 24, 24, 6, 24, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 58, 75, 75, 98, 98, 98, 98, 98, 58, 24, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 98 rigid atoms, others: [33, 34, 35, 36, 9, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 488 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918714 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918714 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918714/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918714 Building REAL300004918715 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918715' /scratch/stefan/7775246/working/building/REAL300004918715 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918715 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918715/0 /scratch/stefan/7775246/working/building/REAL300004918715 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/719 `/scratch/stefan/7775246/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(OCCOC)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918715 none CC#CCC(NC(=O)C1=CC(OC)=C(OCCOC)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 5, 12, 5, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 8, 4, 4, 1, 4, 1, 1, 1, 1, 3, 1, 1, 10, 31, 42, 49, 1, 1, 1, 2, 2, 8, 14, 14, 28, 28, 28, 28, 28, 8, 4, 1, 4, 4, 4, 31, 31, 42, 42, 49, 49, 49, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 13, 14, 45, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918715 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918715 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918715/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918715 Building REAL300004918716 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918716' /scratch/stefan/7775246/working/building/REAL300004918716 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918716 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918716/0 /scratch/stefan/7775246/working/building/REAL300004918716 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/720 `/scratch/stefan/7775246/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(S(=O)(=O)N2CCCC2)C=CS1)C(=O)[O-]) `REAL300004918716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918716 none CC#CCC(NC(=O)C1=C(S(=O)(=O)N2CCCC2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 25, 9, 9, 1, 9, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 1, 1, 1, 25, 39, 39, 69, 69, 69, 69, 69, 25, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 121 rigid atoms, others: [6, 39, 8, 9, 10, 40, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918716 none CC#CCC(NC(=O)C1=C(S(=O)(=O)N2CCCC2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 71, 47, 47, 18, 47, 18, 6, 1, 6, 6, 1, 1, 1, 1, 1, 18, 18, 18, 71, 88, 88, 120, 120, 120, 120, 120, 71, 47, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 120 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918716 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918716 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918716/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918716 Building REAL300004918717 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918717' /scratch/stefan/7775246/working/building/REAL300004918717 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918717 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918717/0 /scratch/stefan/7775246/working/building/REAL300004918717 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/721 `/scratch/stefan/7775246/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC([N+](=O)[O-])=C2)N=N1)C(=O)[O-]) `REAL300004918717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918717 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC([N+](=O)[O-])=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 1, 1, 34, 46, 46, 67, 67, 67, 67, 67, 34, 11, 2, 2, 2, 7, 7, 2, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 343 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918717 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC([N+](=O)[O-])=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 42, 42, 7, 42, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 119, 151, 151, 201, 201, 201, 201, 201, 119, 42, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 946 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918717 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918717 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918717/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918717 Building REAL300004918718 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918718' /scratch/stefan/7775246/working/building/REAL300004918718 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918718 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918718/0 /scratch/stefan/7775246/working/building/REAL300004918718 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/722 `/scratch/stefan/7775246/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C)N=C1C(F)(F)F)C(=O)[O-]) `REAL300004918718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918718 none CC#CCC(NC(=O)C1=CN(C)N=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 31, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 49, 49, 83, 83, 83, 83, 83, 31, 11, 1, 2, 2, 2] 83 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918718 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918718 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918718/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918718 Building REAL300004918719 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918719' /scratch/stefan/7775246/working/building/REAL300004918719 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918719 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918719/0 /scratch/stefan/7775246/working/building/REAL300004918719 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/723 `/scratch/stefan/7775246/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)N=C(C(F)(F)F)N2C(C)C)C(=O)[O-]) `REAL300004918719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918719 none CC#CCC(NC(=O)C1=CC=C2C(=C1)N=C(C(F)(F)F)N2C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 25, 33, 33, 55, 55, 55, 55, 55, 25, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 55 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918719 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918719 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918719/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918719 Building REAL300004918720 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918720' /scratch/stefan/7775246/working/building/REAL300004918720 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918720 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918720/0 /scratch/stefan/7775246/working/building/REAL300004918720 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/724 `/scratch/stefan/7775246/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCCOC)=C1)C(=O)[O-]) `REAL300004918720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918720 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCCOC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 24, 36, 1, 16, 23, 23, 41, 41, 41, 41, 41, 16, 5, 1, 1, 1, 9, 20, 20, 24, 24, 36, 36, 36, 1] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918720 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918720 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918720/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918720 Building REAL300004918721 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918721' /scratch/stefan/7775246/working/building/REAL300004918721 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918721 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918721/0 /scratch/stefan/7775246/working/building/REAL300004918721 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/725 `/scratch/stefan/7775246/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(C)C=C1Br)C(=O)[O-]) `REAL300004918721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918721 none CC#CCC(NC(=O)C(C)OC1=CC=C(C)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 81, 49, 49, 15, 49, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 85, 85, 101, 101, 101, 101, 101, 81, 49, 15, 15, 15, 15, 1, 1, 2, 2, 2, 1] 101 rigid atoms, others: [33, 34, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 451 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918721 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918721 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918721/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918721 Building REAL300004918722 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918722' /scratch/stefan/7775246/working/building/REAL300004918722 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918722 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918722/0 /scratch/stefan/7775246/working/building/REAL300004918722 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/726 `/scratch/stefan/7775246/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(C(=O)C2=CC=C(Cl)C=C2)C=C1)C(=O)[O-]) `REAL300004918722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918722 none CC#CCC(NC(=O)COC1=CC=C(C(=O)C2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 36, 24, 24, 7, 24, 3, 1, 1, 1, 1, 1, 1, 12, 12, 15, 15, 12, 12, 15, 15, 1, 1, 36, 53, 53, 69, 69, 69, 69, 69, 36, 24, 8, 8, 1, 1, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [43, 37, 38, 9, 10, 11, 12, 13, 14, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 411 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918722 none CC#CCC(NC(=O)COC1=CC=C(C(=O)C2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 154, 117, 117, 47, 117, 28, 12, 12, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 154, 173, 173, 201, 201, 201, 201, 201, 154, 117, 47, 47, 15, 15, 1, 1, 1, 1, 15, 15] 201 rigid atoms, others: [39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 901 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918722 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918722 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918722/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918722 Building REAL300004918723 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918723' /scratch/stefan/7775246/working/building/REAL300004918723 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918723 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918723/0 /scratch/stefan/7775246/working/building/REAL300004918723 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/727 `/scratch/stefan/7775246/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(Cl)=CC=C2N1)C(=O)[O-]) `REAL300004918723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918723 none CC#CCC(NC(=O)C1=CC2=CC(Cl)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 43, 43, 66, 66, 66, 66, 66, 35, 11, 1, 1, 1, 1, 1] 66 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918723 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918723 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918723/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918723 Building REAL300004918724 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918724' /scratch/stefan/7775246/working/building/REAL300004918724 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918724 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918724/0 /scratch/stefan/7775246/working/building/REAL300004918724 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/728 `/scratch/stefan/7775246/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004918724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918724 none CC#CCC(NC(=O)C1=CC=C(NC(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 24, 24, 1, 1, 13, 22, 22, 50, 50, 50, 50, 50, 13, 4, 1, 1, 9, 24, 24, 24, 24, 24, 1, 1] 174 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918724 none CC#CCC(NC(=O)C1=CC=C(NC(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 104, 49, 49, 24, 49, 13, 24, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 24, 104, 131, 131, 174, 174, 174, 174, 174, 104, 49, 24, 24, 4, 1, 1, 1, 1, 1, 24, 24] 174 rigid atoms, others: [36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 867 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918724 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918724 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918724/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918724 Building REAL300004918725 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918725' /scratch/stefan/7775246/working/building/REAL300004918725 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918725 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918725/0 /scratch/stefan/7775246/working/building/REAL300004918725 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/729 `/scratch/stefan/7775246/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=NN3N=NN=C3C=C2)CC1)C(=O)[O-]) `REAL300004918725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918725 none CC#CCC(NC(=O)C1CCN(C2=NN3N=NN=C3C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 33, 12, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 33, 52, 52, 69, 69, 69, 69, 69, 33, 13, 1, 1, 1, 1, 1, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 43, 40, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 362 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918725 none CC#CCC(NC(=O)C1CCN(C2=NN3N=NN=C3C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 61, 61, 10, 61, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 121, 153, 153, 201, 201, 201, 201, 201, 121, 61, 10, 10, 10, 10, 10, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 933 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918725 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918725 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918725/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918725 Building REAL300004918726 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918726' /scratch/stefan/7775246/working/building/REAL300004918726 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918726 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918726/0 /scratch/stefan/7775246/working/building/REAL300004918726 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/730 `/scratch/stefan/7775246/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC1=CC=CC=C1)C(=O)[O-]) `REAL300004918726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918726 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 30, 12, 12, 1, 12, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 30, 50, 50, 69, 69, 69, 69, 69, 30, 12, 1, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918726 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 65, 65, 13, 65, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 121, 160, 160, 201, 201, 201, 201, 201, 121, 65, 13, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 983 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918726 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918726 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918726/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918726 Building REAL300004918727 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918727' /scratch/stefan/7775246/working/building/REAL300004918727 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918727 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918727/0 /scratch/stefan/7775246/working/building/REAL300004918727 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/731 `/scratch/stefan/7775246/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2F)O1)C(=O)[O-]) `REAL300004918727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918727 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 41, 41, 11, 41, 41, 41, 10, 29, 40, 40, 72, 72, 72, 72, 72, 29, 10, 1, 1, 1, 1, 10, 41, 41, 37, 41] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918727 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 94, 94, 41, 94, 41, 41, 41, 41, 41, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 136, 163, 163, 201, 201, 201, 201, 201, 136, 94, 41, 41, 41, 41, 10, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 881 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918727 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 75, 40, 40, 10, 40, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 75, 101, 101, 153, 153, 153, 153, 153, 75, 40, 10, 10, 10, 10, 1, 10, 10, 8, 10] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918727 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918727 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918727/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918727 Building REAL300004918728 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918728' /scratch/stefan/7775246/working/building/REAL300004918728 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918728 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918728/0 /scratch/stefan/7775246/working/building/REAL300004918728 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/732 `/scratch/stefan/7775246/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)N=C1)C(=O)[O-]) `REAL300004918728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918728 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 49, 76, 76, 122, 122, 122, 122, 122, 49, 13, 2, 2, 2, 4, 4, 4, 4, 1] 148 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 607 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918728 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 80, 26, 26, 4, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 80, 106, 106, 148, 148, 148, 148, 148, 80, 26, 4, 4, 4, 1, 1, 1, 1, 4] 148 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 694 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918728 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918728 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918728/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918728 Building REAL300004918729 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918729' /scratch/stefan/7775246/working/building/REAL300004918729 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918729 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918729/0 /scratch/stefan/7775246/working/building/REAL300004918729 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/733 `/scratch/stefan/7775246/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2N=C(C)C=C(C)N2N=C1)C(=O)[O-]) `REAL300004918729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918729 none CC#CCC(NC(=O)C1=C2N=C(C)C=C(C)N2N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 39, 39, 61, 61, 61, 61, 61, 28, 11, 2, 2, 2, 1, 2, 2, 2, 1] 61 rigid atoms, others: [32, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918729 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918729 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918729/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918729 Building REAL300004918730 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918730' /scratch/stefan/7775246/working/building/REAL300004918730 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918730 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918730/0 /scratch/stefan/7775246/working/building/REAL300004918730 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/734 `/scratch/stefan/7775246/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Br)C=C2)N=C1)C(=O)[O-]) `REAL300004918730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918730 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Br)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 52, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 52, 76, 76, 122, 122, 122, 122, 122, 52, 12, 2, 2, 2, 4, 4, 4, 4, 1] 149 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 587 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918730 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Br)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 82, 26, 26, 4, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 82, 106, 106, 149, 149, 149, 149, 149, 82, 26, 4, 4, 4, 1, 1, 1, 1, 4] 149 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 683 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918730 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918730 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918730/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918730 Building REAL300004918731 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918731' /scratch/stefan/7775246/working/building/REAL300004918731 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918731 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918731/0 /scratch/stefan/7775246/working/building/REAL300004918731 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/735 `/scratch/stefan/7775246/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(OC(F)(F)F)C=C2N1)C(=O)[O-]) `REAL300004918731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918731 none CC#CCC(NC(=O)C1=CC2=CC=C(OC(F)(F)F)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 27, 27, 27, 1, 1, 1, 22, 35, 35, 63, 63, 63, 63, 63, 22, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918731 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918731 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918731/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918731 Building REAL300004918732 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918732' /scratch/stefan/7775246/working/building/REAL300004918732 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918732 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918732/0 /scratch/stefan/7775246/working/building/REAL300004918732 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/736 `/scratch/stefan/7775246/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CC(=O)N2C=CSC2=N1)C(=O)[O-]) `REAL300004918732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918732 none CC#CCC(NC(=O)CSCC1=CC(=O)N2C=CSC2=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 1, 11, 8, 1, 1, 14, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 186, 155, 155, 76, 155, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 186, 188, 188, 201, 201, 201, 201, 201, 186, 155, 76, 76, 7, 7, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918732 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918732 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918732/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918732 Building REAL300004918733 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918733' /scratch/stefan/7775246/working/building/REAL300004918733 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918733 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918733/0 /scratch/stefan/7775246/working/building/REAL300004918733 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/737 `/scratch/stefan/7775246/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)SC(C2=CC=CO2)=N1)C(=O)[O-]) `REAL300004918733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918733 none CC#CCC(NC(=O)C1=C(C)SC(C2=CC=CO2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 14, 1, 1, 1, 1, 1, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 34, 50, 50, 86, 86, 86, 86, 86, 34, 10, 2, 2, 2, 13, 13, 13] 138 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918733 none CC#CCC(NC(=O)C1=C(C)SC(C2=CC=CO2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 14, 1, 1, 1, 1, 1, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 82, 42, 42, 13, 42, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 82, 108, 108, 138, 138, 138, 138, 138, 82, 42, 13, 13, 13, 1, 1, 1] 138 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918733 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918733 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918733/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918733 Building REAL300004918734 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918734' /scratch/stefan/7775246/working/building/REAL300004918734 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918734 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918734/0 /scratch/stefan/7775246/working/building/REAL300004918734 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/738 `/scratch/stefan/7775246/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(NS(C)(=O)=O)=C1)C(=O)[O-]) `REAL300004918734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918734 none CC#CCC(NC(=O)C1=CC=C(C)C(NS(C)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 14, 5, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 1, 16, 27, 27, 52, 52, 52, 52, 52, 16, 5, 1, 1, 2, 2, 2, 7, 12, 12, 12, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 14, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 288 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918734 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918734 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918734/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918734 Building REAL300004918735 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918735' /scratch/stefan/7775246/working/building/REAL300004918735 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918735 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918735/0 /scratch/stefan/7775246/working/building/REAL300004918735 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/739 `/scratch/stefan/7775246/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-]) `REAL300004918735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918735 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 67, 39, 39, 11, 38, 11, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 67, 84, 84, 112, 112, 112, 112, 112, 67, 39, 11, 11, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918735 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 142, 99, 99, 43, 99, 43, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 142, 162, 162, 201, 201, 201, 201, 201, 142, 99, 43, 43, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 866 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918735 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918735 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918735/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918735 Building REAL300004918736 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918736' /scratch/stefan/7775246/working/building/REAL300004918736 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918736 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918736/0 /scratch/stefan/7775246/working/building/REAL300004918736 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/740 `/scratch/stefan/7775246/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=C(C)C(C)=NN(C)C2=O)S1)C(=O)[O-]) `REAL300004918736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918736 none CC#CCC(NC(=O)C1=C(C)N=C(C2=C(C)C(C)=NN(C)C2=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 5, 8, 8, 5, 1, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 9, 10, 10, 10, 10, 1, 39, 59, 59, 94, 94, 94, 94, 94, 39, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 458 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918736 none CC#CCC(NC(=O)C1=C(C)N=C(C2=C(C)C(C)=NN(C)C2=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 5, 8, 8, 5, 1, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 66, 66, 10, 65, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 141, 166, 166, 201, 201, 201, 201, 201, 141, 66, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 931 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918736 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918736 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918736/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918736 Building REAL300004918737 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918737' /scratch/stefan/7775246/working/building/REAL300004918737 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918737 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918737/0 /scratch/stefan/7775246/working/building/REAL300004918737 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/741 `/scratch/stefan/7775246/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C=C1Br)C(=O)[O-]) `REAL300004918737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918737 none CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 60, 60, 13, 60, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 149, 149, 201, 201, 201, 201, 201, 103, 60, 13, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1015 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918737 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918737 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918737/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918737 Building REAL300004918738 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918738' /scratch/stefan/7775246/working/building/REAL300004918738 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918738 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918738/0 /scratch/stefan/7775246/working/building/REAL300004918738 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/742 `/scratch/stefan/7775246/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC=C2F)S1)C(=O)[O-]) `REAL300004918738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918738 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC=C2F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 45, 29, 29, 9, 28, 9, 1, 1, 1, 1, 1, 1, 11, 11, 2, 11, 11, 11, 1, 45, 65, 65, 79, 79, 79, 79, 79, 45, 29, 9, 9, 1, 1, 11, 11, 9, 11] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918738 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC=C2F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 86, 86, 48, 86, 48, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 127, 155, 155, 201, 201, 201, 201, 201, 127, 86, 48, 48, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918738 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918738 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918738/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918738 Building REAL300004918739 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918739' /scratch/stefan/7775246/working/building/REAL300004918739 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918739 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918739/0 /scratch/stefan/7775246/working/building/REAL300004918739 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/743 `/scratch/stefan/7775246/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)N=C1)C(=O)[O-]) `REAL300004918739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918739 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 1, 29, 39, 39, 58, 58, 58, 58, 58, 29, 13, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 293 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918739 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(C)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 47, 47, 5, 47, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 103, 141, 141, 201, 201, 201, 201, 201, 103, 47, 5, 5, 5, 1, 1, 1, 2, 2, 2, 1, 5] 201 rigid atoms, others: [34, 35, 36, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 41]) total number of confs: 991 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918739 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918739 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918739/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918739 Building REAL300004918740 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918740' /scratch/stefan/7775246/working/building/REAL300004918740 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918740 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918740/0 /scratch/stefan/7775246/working/building/REAL300004918740 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/744 `/scratch/stefan/7775246/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(C(C)C)C=C2)=N1)C(=O)[O-]) `REAL300004918740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918740 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(C(C)C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 41, 12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 3, 3, 1, 41, 63, 63, 118, 118, 118, 118, 118, 41, 12, 1, 3, 3, 11, 12, 12, 12, 12, 12, 12, 3, 3] 160 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918740 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(C(C)C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 74, 31, 30, 3, 31, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 3, 74, 105, 105, 136, 136, 136, 136, 136, 74, 30, 3, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1] 160 rigid atoms, others: [33, 34, 43, 42, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918740 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918740 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918740/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918740 Building REAL300004918741 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918741' /scratch/stefan/7775246/working/building/REAL300004918741 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918741 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918741/0 /scratch/stefan/7775246/working/building/REAL300004918741 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/745 `/scratch/stefan/7775246/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CO2)S1)C(=O)[O-]) `REAL300004918741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918741 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 42, 12, 12, 1, 12, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 11, 11, 11, 11, 1, 42, 61, 61, 101, 101, 101, 101, 101, 42, 12, 4, 4, 1, 4, 4, 11, 11, 11] 201 rigid atoms, others: [6, 8, 9, 10, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918741 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 119, 64, 64, 11, 64, 11, 11, 11, 28, 28, 11, 28, 28, 11, 1, 1, 1, 1, 1, 1, 11, 119, 150, 150, 197, 197, 197, 197, 197, 119, 64, 28, 28, 11, 28, 28, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 950 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918741 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C2=CC=CO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 67, 28, 28, 4, 28, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 28, 28, 28, 28, 4, 67, 89, 89, 124, 124, 124, 124, 124, 67, 28, 1, 1, 1, 1, 1, 28, 28, 28] 201 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 627 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918741 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918741 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918741/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918741 Building REAL300004918742 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918742' /scratch/stefan/7775246/working/building/REAL300004918742 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918742 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918742/0 /scratch/stefan/7775246/working/building/REAL300004918742 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/746 `/scratch/stefan/7775246/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CN1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004918742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918742 none CC#CCC(NC(=O)C1=CC=CN1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 12, 12, 9, 12, 12, 27, 47, 47, 77, 77, 77, 77, 77, 27, 10, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 423 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918742 none CC#CCC(NC(=O)C1=CC=CN1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 54, 54, 12, 54, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 114, 155, 155, 201, 201, 201, 201, 201, 114, 54, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 991 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918742 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918742 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918742/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918742 Building REAL300004918743 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918743' /scratch/stefan/7775246/working/building/REAL300004918743 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918743 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918743/0 /scratch/stefan/7775246/working/building/REAL300004918743 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/747 `/scratch/stefan/7775246/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2=CC=CO2)=NO1)C(=O)[O-]) `REAL300004918743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918743 none CC#CCC(NC(=O)CCC1=NC(C2=CC=CO2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 12, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 96, 73, 73, 19, 72, 8, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 96, 126, 126, 128, 128, 128, 128, 128, 96, 73, 20, 20, 8, 8, 6, 6, 6] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918743 none CC#CCC(NC(=O)CCC1=NC(C2=CC=CO2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 12, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 129, 129, 51, 128, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 158, 197, 197, 201, 201, 201, 201, 201, 158, 129, 51, 51, 32, 33, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 997 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918743 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918743 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918743/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918743 Building REAL300004918744 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918744' /scratch/stefan/7775246/working/building/REAL300004918744 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918744 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918744/0 /scratch/stefan/7775246/working/building/REAL300004918744 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/748 `/scratch/stefan/7775246/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(C)C=C2)N=C1)C(=O)[O-]) `REAL300004918744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918744 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(C)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 2, 3, 4, 4, 1, 1, 49, 75, 75, 115, 115, 115, 115, 115, 49, 12, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 1] 150 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 583 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918744 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(C)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 78, 27, 27, 4, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 78, 101, 101, 150, 150, 150, 150, 150, 78, 27, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4] 150 rigid atoms, others: [34, 35, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41]) total number of confs: 692 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918744 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918744 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918744/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918744 Building REAL300004918745 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918745' /scratch/stefan/7775246/working/building/REAL300004918745 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918745 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918745/0 /scratch/stefan/7775246/working/building/REAL300004918745 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/749 `/scratch/stefan/7775246/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)CCC)=C1)C(=O)[O-]) `REAL300004918745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918745 none CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)CCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 33, 37, 1, 13, 20, 20, 36, 36, 36, 36, 36, 13, 5, 1, 1, 1, 7, 33, 33, 37, 37, 37, 37, 37, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918745 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918745 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918745/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918745 Building REAL300004918746 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918746' /scratch/stefan/7775246/working/building/REAL300004918746 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918746 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918746/0 /scratch/stefan/7775246/working/building/REAL300004918746 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/750 `/scratch/stefan/7775246/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)CC)=C1)C(=O)[O-]) `REAL300004918746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918746 none CC#CCC(NC(=O)C1=CC=CC(NS(=O)(=O)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 26, 1, 13, 22, 22, 43, 43, 43, 43, 43, 13, 5, 1, 1, 1, 8, 26, 26, 26, 26, 26, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918746 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918746 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918746/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918746 Building REAL300004918747 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918747' /scratch/stefan/7775246/working/building/REAL300004918747 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918747 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918747/0 /scratch/stefan/7775246/working/building/REAL300004918747 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/751 `/scratch/stefan/7775246/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C([N+](=O)[O-])C(OC)=C1)C(=O)[O-]) `REAL300004918747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918747 none CC#CCC(NC(=O)C1=CC=C([N+](=O)[O-])C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 28, 46, 46, 95, 95, 95, 95, 95, 28, 7, 1, 1, 4, 4, 4, 1] 113 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 33, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918747 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918747 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918747/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918747 Building REAL300004918748 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918748' /scratch/stefan/7775246/working/building/REAL300004918748 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918748 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918748/0 /scratch/stefan/7775246/working/building/REAL300004918748 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/752 `/scratch/stefan/7775246/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(Br)=C1)C(=O)[O-]) `REAL300004918748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918748 none CC#CCC(NC(=O)C1=CC=C(C)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 34, 34, 65, 65, 65, 65, 65, 24, 7, 1, 1, 2, 2, 2, 1] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918748 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918748 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918748/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918748 Building REAL300004918749 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918749' /scratch/stefan/7775246/working/building/REAL300004918749 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918749 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918749/0 /scratch/stefan/7775246/working/building/REAL300004918749 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/753 `/scratch/stefan/7775246/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(I)=C1)C(=O)[O-]) `REAL300004918749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918749 none CC#CCC(NC(=O)C1=CC=C(C)C(I)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'I', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 18, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 35, 35, 67, 67, 67, 67, 67, 24, 7, 1, 1, 2, 2, 2, 1] 67 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918749 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918749 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918749/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918749 Building REAL300004918750 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918750' /scratch/stefan/7775246/working/building/REAL300004918750 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918750 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918750/0 /scratch/stefan/7775246/working/building/REAL300004918750 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/754 `/scratch/stefan/7775246/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC(OC)=C2O1)C(=O)[O-]) `REAL300004918750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918750 none CC#CCC(NC(=O)C1=CC2=CC=CC(OC)=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 42, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 42, 66, 66, 110, 110, 110, 110, 110, 42, 13, 1, 1, 1, 1, 4, 4, 4] 128 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 34, 16, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918750 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918750 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918750/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918750 Building REAL300004918751 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918751' /scratch/stefan/7775246/working/building/REAL300004918751 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918751 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918751/0 /scratch/stefan/7775246/working/building/REAL300004918751 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/755 `/scratch/stefan/7775246/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(F)(F)F)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918751 none CC#CCC(NC(=O)C1=CC=C(C(F)(F)F)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 18, 24, 24, 36, 36, 36, 36, 36, 18, 6, 1, 1, 1] 36 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918751 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918751 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918751/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918751 Building REAL300004918752 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918752' /scratch/stefan/7775246/working/building/REAL300004918752 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918752 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918752/0 /scratch/stefan/7775246/working/building/REAL300004918752 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/756 `/scratch/stefan/7775246/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(C2=CC=CC=C2Cl)=C1)C(=O)[O-]) `REAL300004918752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918752 none CC#CCC(NC(=O)C1=NOC(C2=CC=CC=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 31, 47, 47, 77, 77, 77, 77, 77, 31, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918752 none CC#CCC(NC(=O)C1=NOC(C2=CC=CC=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 125, 60, 60, 10, 60, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 125, 146, 146, 201, 201, 201, 201, 201, 125, 60, 1, 1, 1, 1, 10] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 870 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918752 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918752 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918752/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918752 Building REAL300004918753 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918753' /scratch/stefan/7775246/working/building/REAL300004918753 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918753 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918753/0 /scratch/stefan/7775246/working/building/REAL300004918753 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/757 `/scratch/stefan/7775246/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(C2=CC=CC=C2F)=C1)C(=O)[O-]) `REAL300004918753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918753 none CC#CCC(NC(=O)C1=NOC(C2=CC=CC=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 28, 45, 45, 66, 66, 66, 66, 66, 28, 10, 13, 13, 13, 13, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918753 none CC#CCC(NC(=O)C1=NOC(C2=CC=CC=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 64, 64, 13, 64, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 130, 153, 153, 201, 201, 201, 201, 201, 130, 64, 1, 1, 1, 1, 13] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 859 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918753 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918753 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918753/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918753 Building REAL300004918754 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918754' /scratch/stefan/7775246/working/building/REAL300004918754 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918754 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918754/0 /scratch/stefan/7775246/working/building/REAL300004918754 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/758 `/scratch/stefan/7775246/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=CC=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918754 none CC#CCC(NC(=O)C1=CC(OC)=CC=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 18, 7, 7, 1, 7, 1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 18, 30, 30, 56, 56, 56, 56, 56, 18, 7, 1, 3, 3, 3, 1, 1] 84 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918754 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918754 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918754/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918754 Building REAL300004918755 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918755' /scratch/stefan/7775246/working/building/REAL300004918755 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918755 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918755/0 /scratch/stefan/7775246/working/building/REAL300004918755 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/759 `/scratch/stefan/7775246/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC=C(OC)C=C12)C(=O)[O-]) `REAL300004918755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918755 none CC#CCC(NC(=O)CC1=CNC2=CC=C(OC)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 82, 43, 43, 8, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 82, 121, 121, 177, 177, 177, 177, 177, 82, 43, 8, 8, 1, 1, 1, 1, 2, 3, 3, 1] 201 rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 913 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918755 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918755 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918755/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918755 Building REAL300004918756 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918756' /scratch/stefan/7775246/working/building/REAL300004918756 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918756 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918756/0 /scratch/stefan/7775246/working/building/REAL300004918756 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/760 `/scratch/stefan/7775246/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOCC1=CC=CC=C1)C(=O)[O-]) `REAL300004918756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918756 none CC#CCC(NC(=O)CCCOCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 190, 187, 187, 100, 187, 83, 48, 14, 4, 1, 1, 1, 1, 1, 1, 1, 190, 199, 199, 201, 201, 201, 201, 201, 190, 187, 100, 100, 83, 83, 48, 48, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 821 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918756 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918756 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918756/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918756 Building REAL300004918757 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918757' /scratch/stefan/7775246/working/building/REAL300004918757 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918757 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918757/0 /scratch/stefan/7775246/working/building/REAL300004918757 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/761 `/scratch/stefan/7775246/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2F)S1)C(=O)[O-]) `REAL300004918757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918757 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 28, 45, 45, 77, 77, 77, 77, 77, 28, 11, 1, 1, 12, 12, 10, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918757 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 68, 68, 12, 68, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 126, 155, 155, 201, 201, 201, 201, 201, 126, 68, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 914 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918757 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918757 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918757/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918757 Building REAL300004918758 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918758' /scratch/stefan/7775246/working/building/REAL300004918758 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918758 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918758/0 /scratch/stefan/7775246/working/building/REAL300004918758 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/762 `/scratch/stefan/7775246/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CS(=O)(=O)C2=CC=C(C)C=C2)C=C1)C(=O)[O-]) `REAL300004918758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918758 none CC#CCC(NC(=O)C1=CC=C(CS(=O)(=O)C2=CC=C(C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 9, 15, 15, 31, 31, 31, 31, 31, 9, 3, 1, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918758 none CC#CCC(NC(=O)C1=CC=C(CS(=O)(=O)C2=CC=C(C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 112, 40, 40, 16, 40, 10, 22, 22, 10, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 22, 22, 112, 146, 146, 201, 201, 201, 201, 201, 112, 40, 22, 22, 10, 10, 1, 1, 2, 2, 2, 1, 1, 22, 22] 201 rigid atoms, others: [39, 40, 44, 13, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 46, 47]) total number of confs: 1061 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918758 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918758 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918758/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918758 Building REAL300004918759 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918759' /scratch/stefan/7775246/working/building/REAL300004918759 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918759 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918759/0 /scratch/stefan/7775246/working/building/REAL300004918759 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/763 `/scratch/stefan/7775246/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CS(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918759 none CC#CCC(NC(=O)C1=CC=CC(CS(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 19, 19, 19, 19, 19, 19, 19, 19, 1, 14, 25, 25, 46, 46, 46, 46, 46, 14, 5, 1, 1, 1, 3, 3, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 44, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918759 none CC#CCC(NC(=O)C1=CC=CC(CS(=O)(=O)C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 57, 57, 19, 57, 19, 19, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 121, 153, 153, 201, 201, 201, 201, 201, 121, 57, 19, 19, 19, 10, 10, 1, 1, 1, 1, 1, 19] 201 rigid atoms, others: [39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 992 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918759 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918759 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918759/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918759 Building REAL300004918760 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918760' /scratch/stefan/7775246/working/building/REAL300004918760 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918760 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918760/0 /scratch/stefan/7775246/working/building/REAL300004918760 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/764 `/scratch/stefan/7775246/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC(C)(C)C)=CC=C1C)C(=O)[O-]) `REAL300004918760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918760 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC(C)(C)C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 22, 9, 9, 1, 9, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 1, 1, 22, 34, 34, 56, 56, 56, 56, 56, 22, 9, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2] 159 rigid atoms, others: [33, 6, 8, 9, 10, 11, 44, 45, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918760 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918760 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918760/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918760 Building REAL300004918761 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918761' /scratch/stefan/7775246/working/building/REAL300004918761 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918761 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918761/0 /scratch/stefan/7775246/working/building/REAL300004918761 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/765 `/scratch/stefan/7775246/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC(C)(C)C)=C1)C(=O)[O-]) `REAL300004918761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918761 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 4, 1, 1, 7, 7, 7, 14, 17, 17, 17, 1, 16, 26, 26, 56, 56, 56, 56, 56, 16, 5, 1, 1, 4, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 14, 15, 49, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918761 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918761 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918761/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918761 Building REAL300004918762 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918762' /scratch/stefan/7775246/working/building/REAL300004918762 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918762 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918762/0 /scratch/stefan/7775246/working/building/REAL300004918762 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/766 `/scratch/stefan/7775246/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NCCOC)=CC=C1C)C(=O)[O-]) `REAL300004918762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918762 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NCCOC)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 17, 9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 9, 20, 22, 33, 1, 1, 1, 1, 17, 29, 29, 46, 46, 46, 46, 46, 17, 9, 1, 9, 20, 20, 22, 22, 33, 33, 33, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 43, 6, 8, 9, 10, 11, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918762 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918762 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918762/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918762 Building REAL300004918763 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918763' /scratch/stefan/7775246/working/building/REAL300004918763 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918763 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918763/0 /scratch/stefan/7775246/working/building/REAL300004918763 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/767 `/scratch/stefan/7775246/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCC2)=CC=C1Cl)C(=O)[O-]) `REAL300004918763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918763 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCC2)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 19, 7, 7, 1, 7, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 26, 1, 1, 1, 1, 19, 30, 30, 56, 56, 56, 56, 56, 19, 7, 1, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 201 rigid atoms, others: [33, 43, 6, 8, 9, 10, 11, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918763 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCC2)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 88, 88, 26, 88, 26, 26, 6, 1, 6, 6, 1, 1, 1, 1, 1, 26, 26, 26, 26, 130, 159, 159, 201, 201, 201, 201, 201, 130, 88, 26, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43]) total number of confs: 894 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918763 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918763 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918763/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918763 Building REAL300004918764 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918764' /scratch/stefan/7775246/working/building/REAL300004918764 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918764 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918764/0 /scratch/stefan/7775246/working/building/REAL300004918764 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/768 `/scratch/stefan/7775246/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(Cl)N(CCCC)N=C1C)C(=O)[O-]) `REAL300004918764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918764 none CC#CCC(NC(=O)C=CC1=C(Cl)N(CCCC)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 5, 5, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 45, 27, 27, 7, 27, 7, 1, 1, 1, 1, 1, 1, 5, 9, 9, 1, 1, 1, 45, 64, 64, 89, 89, 89, 89, 89, 45, 27, 7, 7, 5, 5, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918764 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918764 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918764/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918764 Building REAL300004918765 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918765' /scratch/stefan/7775246/working/building/REAL300004918765 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918765 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918765/0 /scratch/stefan/7775246/working/building/REAL300004918765 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/769 `/scratch/stefan/7775246/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)C=CC2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004918765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918765 none CC#CCC(NC(=O)C1CCN(C(=O)C=CC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 27, 27, 19, 27, 27, 1, 1, 14, 24, 24, 30, 30, 30, 30, 30, 14, 6, 1, 1, 1, 1, 1, 19, 19, 27, 27, 19, 27, 27, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 48, 49, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 254 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918765 none CC#CCC(NC(=O)C1CCN(C(=O)C=CC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 97, 97, 27, 97, 27, 27, 27, 15, 3, 15, 3, 1, 1, 1, 1, 1, 1, 1, 27, 27, 139, 165, 165, 201, 201, 201, 201, 201, 139, 97, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 1, 1, 27, 27, 27, 27] 201 rigid atoms, others: [41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 916 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918765 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918765 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918765/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918765 Building REAL300004918766 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918766' /scratch/stefan/7775246/working/building/REAL300004918766 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918766 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918766/0 /scratch/stefan/7775246/working/building/REAL300004918766 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/770 `/scratch/stefan/7775246/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(Cl)C(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004918766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918766 none CC#CCC(NC(=O)C=CC1=CC=C(Cl)C(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 45, 45, 6, 46, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 120, 151, 151, 201, 201, 201, 201, 201, 120, 46, 6, 6, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 915 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918766 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918766 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918766/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918766 Building REAL300004918767 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918767' /scratch/stefan/7775246/working/building/REAL300004918767 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918767 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918767/0 /scratch/stefan/7775246/working/building/REAL300004918767 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/771 `/scratch/stefan/7775246/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNS(=O)(=O)C1=CC=CC(C(=O)NC(CC#CC)C(=O)[O-])=C1) `REAL300004918767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918767 none C=CCNS(=O)(=O)C1=CC=CC(C(=O)NC(CC#CC)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.1', 'C.1', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 35, 35, 35, 13, 21, 21, 1, 36, 36, 36, 21, 21, 6, 1, 1, 1, 5, 13, 35, 35, 35, 35, 35, 1] 201 rigid atoms, others: [32, 4, 7, 8, 9, 10, 11, 12, 40, 23, 30, 31] set([0, 1, 2, 3, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918767 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918767 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918767/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918767 Building REAL300004918768 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918768' /scratch/stefan/7775246/working/building/REAL300004918768 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918768 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918768/0 /scratch/stefan/7775246/working/building/REAL300004918768 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/772 `/scratch/stefan/7775246/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC)=C1)C(=O)[O-]) `REAL300004918768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918768 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 21, 1, 17, 29, 29, 60, 60, 60, 60, 60, 17, 5, 1, 1, 4, 4, 4, 21, 21, 21, 21, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 14, 15, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918768 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918768 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918768/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918768 Building REAL300004918769 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918769' /scratch/stefan/7775246/working/building/REAL300004918769 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918769 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918769/0 /scratch/stefan/7775246/working/building/REAL300004918769 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/773 `/scratch/stefan/7775246/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC)=CC=C1Cl)C(=O)[O-]) `REAL300004918769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918769 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 20, 7, 7, 1, 7, 1, 1, 1, 1, 2, 2, 2, 9, 1, 1, 1, 1, 20, 38, 38, 71, 71, 71, 71, 71, 20, 7, 1, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918769 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918769 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918769/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918769 Building REAL300004918770 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918770' /scratch/stefan/7775246/working/building/REAL300004918770 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918770 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918770/0 /scratch/stefan/7775246/working/building/REAL300004918770 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/774 `/scratch/stefan/7775246/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004918770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918770 none CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 1, 17, 28, 28, 66, 66, 66, 66, 66, 17, 5, 1, 1, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 14, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918770 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918770 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918770/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918770 Building REAL300004918771 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918771' /scratch/stefan/7775246/working/building/REAL300004918771 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918771 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918771/0 /scratch/stefan/7775246/working/building/REAL300004918771 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/775 `/scratch/stefan/7775246/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCC)=C1)C(=O)[O-]) `REAL300004918771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918771 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 20, 1, 17, 29, 29, 57, 57, 57, 57, 57, 17, 5, 1, 1, 1, 6, 20, 20, 20, 20, 20, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918771 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918771 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918771/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918771 Building REAL300004918772 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918772' /scratch/stefan/7775246/working/building/REAL300004918772 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918772 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918772/0 /scratch/stefan/7775246/working/building/REAL300004918772 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/776 `/scratch/stefan/7775246/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)C)C=C1)C(=O)[O-]) `REAL300004918772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918772 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 1, 1, 14, 23, 23, 53, 53, 53, 53, 53, 14, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 19, 20, 41, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918772 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918772 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918772/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918772 Building REAL300004918773 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918773' /scratch/stefan/7775246/working/building/REAL300004918773 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918773 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918773/0 /scratch/stefan/7775246/working/building/REAL300004918773 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/777 `/scratch/stefan/7775246/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)(C)C)C=C1)C(=O)[O-]) `REAL300004918773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918773 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 14, 22, 22, 48, 48, 48, 48, 48, 14, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 123 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918773 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918773 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918773/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918773 Building REAL300004918774 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918774' /scratch/stefan/7775246/working/building/REAL300004918774 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918774 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918774/0 /scratch/stefan/7775246/working/building/REAL300004918774 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/778 `/scratch/stefan/7775246/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=C(S(=O)(=O)N(CC)CC)C=CC1=O)C(=O)[O-]) `REAL300004918774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918774 none CC#CCC(NC(=O)CN1C=C(S(=O)(=O)N(CC)CC)C=CC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 5, 5, 4, 5, 1, 1, 1, 1, 1, 7, 7, 7, 11, 16, 11, 16, 1, 1, 1, 1, 7, 8, 8, 11, 11, 11, 11, 11, 7, 5, 4, 4, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 28 rigid atoms, others: [36, 8, 9, 10, 11, 12, 47, 48, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918774 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918774 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918774/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918774 Building REAL300004918775 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918775' /scratch/stefan/7775246/working/building/REAL300004918775 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918775 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918775/0 /scratch/stefan/7775246/working/building/REAL300004918775 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/779 `/scratch/stefan/7775246/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004918775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918775 none CC#CCC(NC(=O)C=CC1=CC=C(OC)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 35, 18, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 9, 9, 1, 35, 55, 55, 67, 67, 67, 67, 67, 35, 18, 5, 5, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 47, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 403 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918775 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918775 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918775/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918775 Building REAL300004918776 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918776' /scratch/stefan/7775246/working/building/REAL300004918776 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918776 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918776/0 /scratch/stefan/7775246/working/building/REAL300004918776 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/780 `/scratch/stefan/7775246/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC)C(S(=O)(=O)NC)=C1)C(=O)[O-]) `REAL300004918776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918776 none CC#CCC(NC(=O)C=CC1=CC=C(OC)C(S(=O)(=O)NC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 48, 22, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 6, 6, 6, 14, 1, 48, 76, 76, 106, 106, 106, 106, 106, 48, 22, 5, 5, 1, 1, 3, 3, 3, 14, 14, 14, 14, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 600 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918776 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918776 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918776/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918776 Building REAL300004918777 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918777' /scratch/stefan/7775246/working/building/REAL300004918777 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918777 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918777/0 /scratch/stefan/7775246/working/building/REAL300004918777 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/781 `/scratch/stefan/7775246/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC)C=C1)C(=O)[O-]) `REAL300004918777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918777 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 8, 33, 1, 1, 9, 17, 17, 45, 45, 45, 45, 45, 9, 3, 1, 1, 8, 33, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918777 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918777 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918777/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918777 Building REAL300004918778 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918778' /scratch/stefan/7775246/working/building/REAL300004918778 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918778 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918778/0 /scratch/stefan/7775246/working/building/REAL300004918778 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/782 `/scratch/stefan/7775246/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)CC)C=C1)C(=O)[O-]) `REAL300004918778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918778 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 25, 1, 1, 9, 17, 17, 38, 38, 38, 38, 38, 9, 3, 1, 1, 9, 17, 17, 17, 17, 25, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918778 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918778 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918778/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918778 Building REAL300004918779 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918779' /scratch/stefan/7775246/working/building/REAL300004918779 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918779 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918779/0 /scratch/stefan/7775246/working/building/REAL300004918779 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/783 `/scratch/stefan/7775246/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918779 none CC#CCC(NC(=O)C1=CC=CC=C1C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 4, 32, 56, 56, 83, 83, 83, 83, 83, 32, 9, 1, 1, 1, 1, 4, 4, 4, 4] 113 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918779 none CC#CCC(NC(=O)C1=CC=CC=C1C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 60, 21, 21, 4, 21, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 60, 82, 82, 113, 113, 113, 113, 113, 60, 21, 4, 3, 4, 4, 1, 1, 1, 1] 113 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918779 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918779 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918779/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918779 Building REAL300004918780 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918780' /scratch/stefan/7775246/working/building/REAL300004918780 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918780 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918780/0 /scratch/stefan/7775246/working/building/REAL300004918780 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/784 `/scratch/stefan/7775246/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004918780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918780 none CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 101, 61, 61, 15, 61, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 146, 146, 201, 201, 201, 201, 201, 101, 61, 15, 15, 15, 15, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1012 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918780 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918780 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918780/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918780 Building REAL300004918781 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918781' /scratch/stefan/7775246/working/building/REAL300004918781 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918781 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918781/0 /scratch/stefan/7775246/working/building/REAL300004918781 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/785 `/scratch/stefan/7775246/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918781 none CC#CCC(NC(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 38, 38, 66, 66, 66, 66, 66, 27, 7, 1, 1, 1] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918781 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918781 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918781/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918781 Building REAL300004918782 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918782' /scratch/stefan/7775246/working/building/REAL300004918782 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918782 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918782/0 /scratch/stefan/7775246/working/building/REAL300004918782 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/786 `/scratch/stefan/7775246/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=O)C3=CC=CC=C3S(=O)(=O)C2=C1)C(=O)[O-]) `REAL300004918782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918782 none CC#CCC(NC(=O)C1=CC=C2C(=O)C3=CC=CC=C3S(=O)(=O)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 38, 38, 59, 59, 59, 59, 59, 28, 7, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 7, 34, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918782 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918782 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918782/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918782 Building REAL300004918783 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918783' /scratch/stefan/7775246/working/building/REAL300004918783 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918783 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918783/0 /scratch/stefan/7775246/working/building/REAL300004918783 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/787 `/scratch/stefan/7775246/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2)CCCC1)C(=O)[O-]) `REAL300004918783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918783 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 43, 11, 11, 1, 11, 1, 1, 5, 5, 1, 1, 5, 5, 1, 1, 1, 1, 43, 68, 68, 128, 128, 128, 128, 128, 43, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 164 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 16, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 602 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918783 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 70, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 70, 102, 102, 164, 164, 164, 164, 164, 70, 23, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 164 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 777 number of broken/clashed sets: 150 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918783 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918783 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918783/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918783 Building REAL300004918784 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918784' /scratch/stefan/7775246/working/building/REAL300004918784 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918784 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918784/0 /scratch/stefan/7775246/working/building/REAL300004918784 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/788 `/scratch/stefan/7775246/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CCCC2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918784 none CC#CCC(NC(=O)C1=CC=C(N2CCCC2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 2, 2, 1, 26, 36, 36, 66, 66, 66, 66, 66, 26, 7, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1] 66 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 17, 18, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918784 none CC#CCC(NC(=O)C1=CC=C(N2CCCC2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 26, 7, 7, 1, 7, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 26, 36, 36, 66, 66, 66, 66, 66, 26, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2] 66 rigid atoms, others: [34, 35, 36, 37, 39, 41, 11, 12, 13, 14, 15, 16, 40, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918784 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918784 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918784/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918784 Building REAL300004918785 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918785' /scratch/stefan/7775246/working/building/REAL300004918785 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918785 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918785/0 /scratch/stefan/7775246/working/building/REAL300004918785 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/789 `/scratch/stefan/7775246/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CNC2=CC=CC=C12)C(=O)[O-]) `REAL300004918785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918785 none CC#CCC(NC(=O)CCCC1=CNC2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 68, 68, 17, 68, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 145, 145, 201, 201, 201, 201, 201, 106, 68, 17, 17, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1028 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918785 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918785 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918785/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918785 Building REAL300004918786 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918786' /scratch/stefan/7775246/working/building/REAL300004918786 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918786 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918786/0 /scratch/stefan/7775246/working/building/REAL300004918786 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/790 `/scratch/stefan/7775246/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004918786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918786 none CC#CCC(NC(=O)C1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 27, 38, 38, 70, 70, 70, 70, 70, 27, 7, 1, 1, 1, 1] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918786 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918786 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918786/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918786 Building REAL300004918787 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918787' /scratch/stefan/7775246/working/building/REAL300004918787 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918787 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918787/0 /scratch/stefan/7775246/working/building/REAL300004918787 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/791 `/scratch/stefan/7775246/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(CC)CC)=C1)C(=O)[O-]) `REAL300004918787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918787 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(CC)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 21, 12, 21, 1, 14, 22, 22, 36, 36, 36, 36, 36, 14, 5, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 45, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918787 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918787 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918787/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918787 Building REAL300004918788 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918788' /scratch/stefan/7775246/working/building/REAL300004918788 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918788 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918788/0 /scratch/stefan/7775246/working/building/REAL300004918788 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/792 `/scratch/stefan/7775246/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1I)C(=O)[O-]) `REAL300004918788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918788 none CC#CCC(NC(=O)C1=CC=CC=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 23, 36, 36, 52, 52, 52, 52, 52, 23, 7, 1, 1, 1, 1] 52 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 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/7775246/working/building/REAL300004918788 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918788 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918788/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918788 Building REAL300004918789 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918789' /scratch/stefan/7775246/working/building/REAL300004918789 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918789 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918789/0 /scratch/stefan/7775246/working/building/REAL300004918789 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/793 `/scratch/stefan/7775246/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CS2)C=C1)C(=O)[O-]) `REAL300004918789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918789 none CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 18, 18, 18, 42, 42, 42, 42, 1, 1, 7, 12, 12, 23, 23, 23, 23, 23, 7, 3, 1, 1, 42, 42, 42, 1, 1] 201 rigid atoms, others: [33, 34, 38, 6, 39, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918789 none CC#CCC(NC(=O)C1=CC=C([N-]S(=O)(=O)C2=CC=CS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 72, 72, 32, 72, 32, 42, 42, 20, 6, 1, 6, 6, 1, 1, 1, 1, 1, 42, 42, 103, 145, 145, 201, 201, 201, 201, 201, 103, 72, 42, 42, 1, 1, 1, 42, 42] 201 rigid atoms, others: [35, 36, 37, 13, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 1017 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918789 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918789 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918789/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918789 Building REAL300004918790 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918790' /scratch/stefan/7775246/working/building/REAL300004918790 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918790 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918790/0 /scratch/stefan/7775246/working/building/REAL300004918790 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/794 `/scratch/stefan/7775246/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCC2)=C1)C(=O)[O-]) `REAL300004918790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918790 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 17, 25, 25, 43, 43, 43, 43, 43, 17, 5, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 46, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918790 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 62, 62, 22, 62, 22, 22, 22, 22, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 22, 125, 160, 160, 201, 201, 201, 201, 201, 125, 62, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 45, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 972 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918790 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918790 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918790/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918790 Building REAL300004918791 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918791' /scratch/stefan/7775246/working/building/REAL300004918791 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918791 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918791/0 /scratch/stefan/7775246/working/building/REAL300004918791 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/795 `/scratch/stefan/7775246/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918791 none CC#CCC(NC(=O)C1=CC=CC(OC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 15, 15, 8, 15, 15, 1, 13, 20, 20, 31, 31, 31, 31, 31, 13, 5, 1, 1, 1, 15, 15, 11, 15, 15, 1] 201 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918791 none CC#CCC(NC(=O)C1=CC=CC(OC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 47, 47, 15, 47, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 15, 102, 138, 138, 201, 201, 201, 201, 201, 102, 47, 15, 15, 15, 1, 1, 1, 1, 1, 15] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 948 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918791 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918791 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918791/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918791 Building REAL300004918792 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918792' /scratch/stefan/7775246/working/building/REAL300004918792 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918792 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918792/0 /scratch/stefan/7775246/working/building/REAL300004918792 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/796 `/scratch/stefan/7775246/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC(Cl)=CC=C1Cl)C(=O)[O-]) `REAL300004918792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918792 none CC#CCC(NC(=O)CSC1=CC(Cl)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 114, 74, 74, 25, 74, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114, 157, 157, 201, 201, 201, 201, 201, 114, 74, 25, 25, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 1045 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918792 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918792 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918792/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918792 Building REAL300004918793 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918793' /scratch/stefan/7775246/working/building/REAL300004918793 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918793 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918793/0 /scratch/stefan/7775246/working/building/REAL300004918793 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/797 `/scratch/stefan/7775246/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N2CCCC2)=C1)C(=O)[O-]) `REAL300004918793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918793 none CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 1, 17, 26, 26, 69, 69, 69, 69, 69, 17, 5, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [33, 34, 43, 6, 8, 9, 10, 11, 12, 13, 14, 22] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918793 none CC#CCC(NC(=O)C1=CC=C(Cl)C(S(=O)(=O)N2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 44, 44, 16, 44, 16, 16, 16, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 1, 16, 110, 139, 139, 201, 201, 201, 201, 201, 110, 44, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43]) total number of confs: 957 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918793 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918793 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918793/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918793 Building REAL300004918794 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918794' /scratch/stefan/7775246/working/building/REAL300004918794 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918794 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918794/0 /scratch/stefan/7775246/working/building/REAL300004918794 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/798 `/scratch/stefan/7775246/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)S(=O)(=O)C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004918794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918794 none CC#CCC(NC(=O)C(C)S(=O)(=O)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 48, 48, 10, 48, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 147, 147, 201, 201, 201, 201, 201, 108, 48, 10, 10, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 995 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918794 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918794 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918794/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918794 Building REAL300004918795 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918795' /scratch/stefan/7775246/working/building/REAL300004918795 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918795 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918795/0 /scratch/stefan/7775246/working/building/REAL300004918795 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/799 `/scratch/stefan/7775246/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC(NC(=O)C2=CC=CO2)=C1)C(=O)[O-]) `REAL300004918795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918795 none CC#CCC(NC(=O)COC1=CC=CC(NC(=O)C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 43, 36, 36, 14, 36, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 1, 43, 68, 68, 87, 87, 87, 87, 87, 43, 36, 14, 14, 1, 1, 1, 9, 15, 15, 15, 1] 201 rigid atoms, others: [43, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 481 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918795 none CC#CCC(NC(=O)COC1=CC=CC(NC(=O)C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 140, 140, 79, 140, 48, 15, 15, 15, 15, 15, 5, 4, 1, 4, 1, 1, 1, 1, 1, 15, 152, 169, 169, 201, 201, 201, 201, 201, 152, 140, 79, 79, 15, 15, 15, 5, 1, 1, 1, 15] 201 rigid atoms, others: [40, 41, 42, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 827 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918795 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918795 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918795/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918795 Building REAL300004918796 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918796' /scratch/stefan/7775246/working/building/REAL300004918796 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918796 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918796/0 /scratch/stefan/7775246/working/building/REAL300004918796 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/800 `/scratch/stefan/7775246/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(OC)C=C(OC)C(OC)=C2N1)C(=O)[O-]) `REAL300004918796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918796 none CC#CCC(NC(=O)C1=CC2=C(OC)C=C(OC)C(OC)=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 12, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 3, 1, 1, 1, 3, 1, 1, 5, 1, 1, 23, 37, 37, 62, 62, 62, 62, 62, 23, 9, 1, 3, 3, 3, 1, 4, 4, 4, 6, 6, 6, 1] 201 rigid atoms, others: [33, 37, 6, 8, 9, 10, 11, 12, 14, 15, 16, 18, 19, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918796 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918796 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918796/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918796 Building REAL300004918797 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918797' /scratch/stefan/7775246/working/building/REAL300004918797 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918797 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918797/0 /scratch/stefan/7775246/working/building/REAL300004918797 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/801 `/scratch/stefan/7775246/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(OC(F)F)=C1)C(=O)[O-]) `REAL300004918797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918797 none CC#CCC(NC(=O)C1=CC=C(OC)C(OC(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 9, 21, 21, 1, 13, 21, 21, 34, 34, 34, 34, 34, 13, 5, 1, 1, 3, 3, 3, 21, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 14, 15, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918797 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918797 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918797/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918797 Building REAL300004918798 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918798' /scratch/stefan/7775246/working/building/REAL300004918798 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918798 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918798/0 /scratch/stefan/7775246/working/building/REAL300004918798 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/802 `/scratch/stefan/7775246/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C=C1)C(=O)[O-]) `REAL300004918798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918798 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 38, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 38, 57, 57, 90, 90, 90, 90, 90, 38, 11, 6, 6, 6, 6, 1, 1] 136 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918798 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 86, 39, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 86, 105, 105, 136, 136, 136, 136, 136, 86, 38, 1, 1, 1, 1, 6, 6] 136 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918798 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918798 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918798/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918798 Building REAL300004918799 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918799' /scratch/stefan/7775246/working/building/REAL300004918799 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918799 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918799/0 /scratch/stefan/7775246/working/building/REAL300004918799 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/803 `/scratch/stefan/7775246/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1)C(=O)[O-]) `REAL300004918799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918799 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 33, 11, 11, 1, 11, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 33, 43, 43, 65, 65, 65, 65, 65, 33, 11, 4, 4, 4, 4, 1, 1] 68 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918799 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 45, 21, 21, 4, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 45, 54, 54, 68, 68, 68, 68, 68, 45, 21, 1, 1, 1, 1, 4, 4] 68 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918799 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918799 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918799/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918799 Building REAL300004918800 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918800' /scratch/stefan/7775246/working/building/REAL300004918800 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918800 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918800/0 /scratch/stefan/7775246/working/building/REAL300004918800 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/804 `/scratch/stefan/7775246/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCC2)O1)C(=O)[O-]) `REAL300004918800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918800 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCC2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 22, 9, 8, 1, 8, 1, 1, 1, 1, 1, 8, 8, 8, 36, 37, 36, 36, 1, 22, 37, 37, 65, 65, 65, 65, 65, 22, 9, 1, 1, 36, 36, 37, 37, 37, 36, 37, 36] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918800 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCC2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 92, 92, 34, 91, 34, 34, 34, 6, 1, 6, 6, 1, 1, 1, 1, 1, 34, 137, 165, 165, 201, 201, 201, 201, 201, 137, 92, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 867 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918800 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918800 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918800/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918800 Building REAL300004918801 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918801' /scratch/stefan/7775246/working/building/REAL300004918801 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918801 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918801/0 /scratch/stefan/7775246/working/building/REAL300004918801 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/805 `/scratch/stefan/7775246/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOCCC1=CC=CC=C1)C(=O)[O-]) `REAL300004918801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918801 none CC#CCC(NC(=O)CCCOCCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 168, 161, 161, 104, 161, 83, 47, 17, 5, 3, 1, 1, 1, 1, 1, 1, 1, 168, 191, 191, 201, 201, 201, 201, 201, 168, 161, 104, 104, 83, 83, 47, 47, 5, 5, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 990 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918801 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918801 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918801/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918801 Building REAL300004918802 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918802' /scratch/stefan/7775246/working/building/REAL300004918802 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918802 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918802/0 /scratch/stefan/7775246/working/building/REAL300004918802 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/806 `/scratch/stefan/7775246/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)C)O1)C(=O)[O-]) `REAL300004918802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918802 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 25, 9, 10, 1, 10, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 1, 25, 40, 40, 71, 71, 71, 71, 71, 25, 10, 1, 1, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918802 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918802 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918802/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918802 Building REAL300004918803 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918803' /scratch/stefan/7775246/working/building/REAL300004918803 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918803 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918803/0 /scratch/stefan/7775246/working/building/REAL300004918803 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/807 `/scratch/stefan/7775246/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(N2C=NN=N2)C=CS1)C(=O)[O-]) `REAL300004918803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918803 none CC#CCC(NC(=O)C1=C(N2C=NN=N2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 8, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 35, 10, 10, 1, 10, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 35, 54, 54, 92, 92, 92, 92, 92, 35, 10, 9, 1, 1] 127 rigid atoms, others: [6, 8, 9, 10, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918803 none CC#CCC(NC(=O)C1=C(N2C=NN=N2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 8, 8, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 61, 29, 29, 9, 29, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 61, 86, 86, 127, 127, 127, 127, 127, 61, 29, 1, 9, 9] 127 rigid atoms, others: [9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918803 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918803 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918803/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918803 Building REAL300004918804 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918804' /scratch/stefan/7775246/working/building/REAL300004918804 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918804 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918804/0 /scratch/stefan/7775246/working/building/REAL300004918804 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/808 `/scratch/stefan/7775246/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC=CC=C2N1)C(=O)[O-]) `REAL300004918804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918804 none CC#CCC(NC(=O)C1=C(Cl)C2=CC=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 33, 33, 57, 57, 57, 57, 57, 22, 6, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918804 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918804 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918804/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918804 Building REAL300004918805 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918805' /scratch/stefan/7775246/working/building/REAL300004918805 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918805 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918805/0 /scratch/stefan/7775246/working/building/REAL300004918805 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/809 `/scratch/stefan/7775246/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=O)N(C(C)C)S(=O)(=O)C2=C1)C(=O)[O-]) `REAL300004918805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918805 none CC#CCC(NC(=O)C1=CC=C2C(=O)N(C(C)C)S(=O)(=O)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 14, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 31, 51, 51, 101, 101, 101, 101, 101, 31, 7, 1, 1, 11, 12, 12, 12, 12, 12, 12, 1] 180 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918805 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918805 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918805/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918805 Building REAL300004918806 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918806' /scratch/stefan/7775246/working/building/REAL300004918806 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918806 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918806/0 /scratch/stefan/7775246/working/building/REAL300004918806 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/810 `/scratch/stefan/7775246/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2)=NO1)C(=O)[O-]) `REAL300004918806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918806 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 44, 13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 1, 1, 44, 75, 75, 124, 124, 124, 124, 124, 44, 13, 1, 7, 7, 7, 7, 7, 7, 7] 164 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918806 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 111, 55, 55, 7, 55, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 111, 130, 130, 164, 164, 164, 164, 164, 111, 55, 7, 1, 1, 2, 2, 2, 1, 1] 164 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918806 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918806 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918806/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918806 Building REAL300004918807 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918807' /scratch/stefan/7775246/working/building/REAL300004918807 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918807 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918807/0 /scratch/stefan/7775246/working/building/REAL300004918807 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/811 `/scratch/stefan/7775246/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-]) `REAL300004918807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918807 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 40, 24, 24, 9, 23, 9, 1, 1, 1, 1, 1, 1, 12, 12, 3, 12, 12, 12, 1, 40, 55, 55, 69, 69, 69, 69, 69, 40, 24, 10, 9, 1, 1, 12, 12, 11, 12] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918807 none CC#CCC(NC(=O)C=CC1=CC=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 90, 90, 57, 90, 57, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 135, 163, 163, 201, 201, 201, 201, 201, 135, 90, 57, 57, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 912 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918807 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918807 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918807/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918807 Building REAL300004918808 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918808' /scratch/stefan/7775246/working/building/REAL300004918808 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004918808 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918808/0 /scratch/stefan/7775246/working/building/REAL300004918808 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/812 `/scratch/stefan/7775246/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)(C)C)O1)C(=O)[O-]) `REAL300004918808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918808 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC(C)(C)C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 18, 6, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 23, 28, 28, 28, 1, 18, 28, 28, 42, 42, 42, 42, 42, 18, 7, 1, 1, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918808 /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `1' /scratch/stefan/7775246/working/building/REAL300004918808/1 /scratch/stefan/7775246/working/building/REAL300004918808 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/813 `/scratch/stefan/7775246/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C(C)(C)C)O1)C(=O)[O-]) `REAL300004918808.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004918808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918808 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C(C)(C)C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 17, 7, 8, 1, 8, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 1, 17, 29, 29, 45, 45, 45, 45, 45, 17, 8, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918808 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918808 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918808/0.* 1: /scratch/stefan/7775246/working/building/REAL300004918808/1.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918808 Building REAL300004918809 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918809' /scratch/stefan/7775246/working/building/REAL300004918809 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004918809 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918809/0 /scratch/stefan/7775246/working/building/REAL300004918809 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/814 `/scratch/stefan/7775246/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC)O1)C(=O)[O-]) `REAL300004918809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918809 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 23, 8, 9, 1, 9, 1, 1, 1, 1, 1, 6, 6, 6, 28, 1, 23, 38, 38, 78, 78, 78, 78, 78, 23, 9, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918809 /scratch/stefan/7775246/working /scratch/stefan/7775246 mkdir: created directory `1' /scratch/stefan/7775246/working/building/REAL300004918809/1 /scratch/stefan/7775246/working/building/REAL300004918809 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/815 `/scratch/stefan/7775246/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C)O1)C(=O)[O-]) `REAL300004918809.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004918809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918809 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 23, 8, 9, 1, 9, 1, 1, 1, 1, 1, 6, 6, 6, 19, 1, 23, 37, 37, 73, 73, 73, 73, 73, 23, 9, 1, 1, 19, 19, 19] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918809 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918809 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918809/0.* 1: /scratch/stefan/7775246/working/building/REAL300004918809/1.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918809 Building REAL300004918810 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918810' /scratch/stefan/7775246/working/building/REAL300004918810 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918810 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918810/0 /scratch/stefan/7775246/working/building/REAL300004918810 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/816 `/scratch/stefan/7775246/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC(C(C)(C)C)=NO1)C(=O)[O-]) `REAL300004918810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918810 none CC#CCC(NC(=O)CCCC1=NC(C(C)(C)C)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 89, 59, 59, 22, 59, 11, 9, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 89, 114, 114, 148, 148, 148, 148, 148, 89, 59, 22, 22, 11, 11, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 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: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918810 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918810 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918810/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918810 Building REAL300004918811 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918811' /scratch/stefan/7775246/working/building/REAL300004918811 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918811 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918811/0 /scratch/stefan/7775246/working/building/REAL300004918811 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/817 `/scratch/stefan/7775246/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC(C2=CC=C(Cl)C=C2)=NO1)C(=O)[O-]) `REAL300004918811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918811 none CC#CCC(NC(=O)CCCC1=NC(C2=CC=C(Cl)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 183, 180, 180, 40, 180, 17, 9, 1, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 183, 188, 188, 200, 200, 200, 200, 200, 183, 180, 40, 40, 17, 17, 9, 9, 4, 4, 4, 4] 201 rigid atoms, others: [10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918811 none CC#CCC(NC(=O)CCCC1=NC(C2=CC=C(Cl)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 184, 182, 182, 47, 182, 24, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 184, 188, 188, 201, 201, 201, 201, 201, 184, 182, 47, 47, 24, 24, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918811 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918811 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918811/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918811 Building REAL300004918812 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918812' /scratch/stefan/7775246/working/building/REAL300004918812 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918812 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918812/0 /scratch/stefan/7775246/working/building/REAL300004918812 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/818 `/scratch/stefan/7775246/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(CC2=CC=C(F)C=C2)S1)C(=O)[O-]) `REAL300004918812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918812 none CC#CCC(NC(=O)C1=C(C)N=C(CC2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 1, 21, 34, 34, 54, 54, 54, 54, 54, 21, 9, 2, 2, 2, 8, 8, 16, 16, 16, 16] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918812 none CC#CCC(NC(=O)C1=C(C)N=C(CC2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 57, 57, 16, 57, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 119, 157, 157, 201, 201, 201, 201, 201, 119, 57, 16, 16, 16, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 970 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918812 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918812 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918812/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918812 Building REAL300004918813 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918813' /scratch/stefan/7775246/working/building/REAL300004918813 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918813 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918813/0 /scratch/stefan/7775246/working/building/REAL300004918813 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/819 `/scratch/stefan/7775246/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(CC)CC)=CC=C1OC)C(=O)[O-]) `REAL300004918813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918813 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(CC)CC)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 16, 9, 9, 1, 9, 1, 1, 1, 1, 8, 8, 8, 16, 30, 16, 32, 1, 1, 1, 1, 3, 16, 25, 25, 36, 36, 36, 36, 36, 16, 9, 1, 30, 30, 30, 30, 30, 32, 32, 32, 32, 32, 1, 1, 4, 4, 4] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 45, 46, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918813 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918813 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918813/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918813 Building REAL300004918814 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918814' /scratch/stefan/7775246/working/building/REAL300004918814 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918814 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918814/0 /scratch/stefan/7775246/working/building/REAL300004918814 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/820 `/scratch/stefan/7775246/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)N(CC)CC)CC1)C(=O)[O-]) `REAL300004918814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918814 none CC#CCC(NC(=O)C1CCN(C(=O)N(CC)CC)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 7, 5, 5, 1, 1, 14, 20, 20, 31, 31, 31, 31, 31, 14, 6, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 1, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 46, 47, 48, 49, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918814 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918814 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918814/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918814 Building REAL300004918815 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918815' /scratch/stefan/7775246/working/building/REAL300004918815 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918815 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918815/0 /scratch/stefan/7775246/working/building/REAL300004918815 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/821 `/scratch/stefan/7775246/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC(Cl)=CC=C2N1)C(=O)[O-]) `REAL300004918815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918815 none CC#CCC(NC(=O)C1=C(Cl)C2=CC(Cl)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 34, 34, 60, 60, 60, 60, 60, 23, 6, 1, 1, 1, 1] 60 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918815 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918815 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918815/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918815 Building REAL300004918816 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918816' /scratch/stefan/7775246/working/building/REAL300004918816 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918816 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918816/0 /scratch/stefan/7775246/working/building/REAL300004918816 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/822 `/scratch/stefan/7775246/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC([N+](=O)[O-])=C2)C=C1)C(=O)[O-]) `REAL300004918816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918816 none CC#CCC(NC(=O)C1=NN(C2=CC=CC([N+](=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 37, 11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 1, 1, 37, 57, 57, 98, 98, 98, 98, 98, 37, 11, 7, 7, 2, 7, 1, 1] 168 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918816 none CC#CCC(NC(=O)C1=NN(C2=CC=CC([N+](=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 101, 44, 44, 7, 44, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 101, 126, 126, 168, 168, 168, 168, 168, 101, 44, 1, 1, 1, 1, 7, 7] 168 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 758 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918816 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918816 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918816/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918816 Building REAL300004918817 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918817' /scratch/stefan/7775246/working/building/REAL300004918817 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918817 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918817/0 /scratch/stefan/7775246/working/building/REAL300004918817 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/823 `/scratch/stefan/7775246/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)NC2=CC=C(Br)C=C21)C(=O)[O-]) `REAL300004918817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918817 none CC#CCC(NC(=O)CC1=C(C)NC2=CC=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 95, 37, 37, 6, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 133, 133, 201, 201, 201, 201, 201, 95, 37, 6, 6, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 960 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918817 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918817 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918817/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918817 Building REAL300004918818 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918818' /scratch/stefan/7775246/working/building/REAL300004918818 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918818 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918818/0 /scratch/stefan/7775246/working/building/REAL300004918818 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/824 `/scratch/stefan/7775246/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC(Br)=CC=C2N1)C(=O)[O-]) `REAL300004918818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918818 none CC#CCC(NC(=O)C1=C(Cl)C2=CC(Br)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 34, 34, 60, 60, 60, 60, 60, 23, 6, 1, 1, 1, 1] 60 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918818 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918818 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918818/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918818 Building REAL300004918819 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918819' /scratch/stefan/7775246/working/building/REAL300004918819 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918819 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918819/0 /scratch/stefan/7775246/working/building/REAL300004918819 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/825 `/scratch/stefan/7775246/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC(F)=CC=C2N1)C(=O)[O-]) `REAL300004918819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918819 none CC#CCC(NC(=O)C1=C(Cl)C2=CC(F)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 31, 31, 58, 58, 58, 58, 58, 21, 6, 1, 1, 1, 1] 58 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918819 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918819 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918819/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918819 Building REAL300004918820 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918820' /scratch/stefan/7775246/working/building/REAL300004918820 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918820 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918820/0 /scratch/stefan/7775246/working/building/REAL300004918820 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/826 `/scratch/stefan/7775246/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(C)O2)=N1)C(=O)[O-]) `REAL300004918820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918820 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(C)O2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 5, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 35, 11, 12, 1, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 35, 52, 52, 85, 85, 85, 85, 85, 35, 12, 1, 12, 12, 12, 12, 12] 149 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918820 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(C)O2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 5, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 87, 45, 46, 12, 46, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 87, 112, 112, 149, 149, 149, 149, 149, 87, 46, 12, 1, 1, 1, 1, 1] 149 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918820 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918820 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918820/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918820 Building REAL300004918821 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918821' /scratch/stefan/7775246/working/building/REAL300004918821 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918821 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918821/0 /scratch/stefan/7775246/working/building/REAL300004918821 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/827 `/scratch/stefan/7775246/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(CC2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918821 none CC#CCC(NC(=O)CC1=CSC(CC2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 30, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 1, 30, 30, 30, 52, 52, 52, 52, 52, 30, 15, 5, 5, 1, 7, 7, 11, 11, 11, 11, 11] 121 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918821 none CC#CCC(NC(=O)CC1=CSC(CC2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 103, 66, 66, 23, 66, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 103, 103, 103, 121, 121, 121, 121, 121, 103, 66, 23, 23, 11, 3, 3, 1, 1, 1, 1, 1] 121 rigid atoms, others: [36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918821 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918821 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918821/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918821 Building REAL300004918822 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918822' /scratch/stefan/7775246/working/building/REAL300004918822 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918822 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918822/0 /scratch/stefan/7775246/working/building/REAL300004918822 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/828 `/scratch/stefan/7775246/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(CC2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004918822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918822 none CC#CCC(NC(=O)C1=C(C)N=C(CC2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 1, 21, 34, 34, 56, 56, 56, 56, 56, 21, 9, 2, 2, 2, 8, 8, 17, 17, 17, 17, 17] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918822 none CC#CCC(NC(=O)C1=C(C)N=C(CC2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 58, 58, 17, 58, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 17, 118, 155, 155, 201, 201, 201, 201, 201, 118, 58, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918822 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918822 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918822/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918822 Building REAL300004918823 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918823' /scratch/stefan/7775246/working/building/REAL300004918823 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918823 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918823/0 /scratch/stefan/7775246/working/building/REAL300004918823 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/829 `/scratch/stefan/7775246/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(OCC)C=C2N1)C(=O)[O-]) `REAL300004918823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918823 none CC#CCC(NC(=O)C1=CC2=CC=C(OCC)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 15, 1, 1, 1, 38, 59, 59, 113, 113, 113, 113, 113, 38, 12, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [32, 38, 6, 39, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 562 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918823 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918823 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918823/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918823 Building REAL300004918824 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918824' /scratch/stefan/7775246/working/building/REAL300004918824 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918824 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918824/0 /scratch/stefan/7775246/working/building/REAL300004918824 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/830 `/scratch/stefan/7775246/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(CC2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004918824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918824 none CC#CCC(NC(=O)C1=CSC(CC2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 8, 18, 18, 12, 18, 18, 1, 18, 29, 29, 57, 57, 57, 57, 57, 18, 8, 1, 8, 8, 18, 18, 12, 18, 18] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918824 none CC#CCC(NC(=O)C1=CSC(CC2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 106, 50, 50, 18, 50, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 106, 144, 144, 201, 201, 201, 201, 201, 106, 50, 18, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 979 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918824 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918824 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918824/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918824 Building REAL300004918825 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918825' /scratch/stefan/7775246/working/building/REAL300004918825 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918825 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918825/0 /scratch/stefan/7775246/working/building/REAL300004918825 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/831 `/scratch/stefan/7775246/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(=O)NC2=CC(F)=CC=C21)C(=O)[O-]) `REAL300004918825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918825 none CC#CCC(NC(=O)C1=CC(=O)NC2=CC(F)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 51, 51, 83, 83, 83, 83, 83, 36, 9, 1, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918825 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918825 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918825/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918825 Building REAL300004918826 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918826' /scratch/stefan/7775246/working/building/REAL300004918826 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918826 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918826/0 /scratch/stefan/7775246/working/building/REAL300004918826 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/832 `/scratch/stefan/7775246/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C2=CC=CC=C2N1)C(=O)[O-]) `REAL300004918826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918826 none CC#CCC(NC(=O)C1=C(Br)C2=CC=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 32, 32, 55, 55, 55, 55, 55, 22, 6, 1, 1, 1, 1, 1] 55 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918826 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918826 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918826/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918826 Building REAL300004918827 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918827' /scratch/stefan/7775246/working/building/REAL300004918827 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918827 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918827/0 /scratch/stefan/7775246/working/building/REAL300004918827 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/833 `/scratch/stefan/7775246/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(CCCC2=O)O1)C(=O)[O-]) `REAL300004918827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918827 none CC#CCC(NC(=O)C1=C(C)C2=C(CCCC2=O)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 5, 5, 5, 1, 11, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 39, 39, 57, 57, 57, 57, 57, 29, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 296 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918827 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918827 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918827/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918827 Building REAL300004918828 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918828' /scratch/stefan/7775246/working/building/REAL300004918828 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918828 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918828/0 /scratch/stefan/7775246/working/building/REAL300004918828 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/834 `/scratch/stefan/7775246/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC=CC=C2N1C)C(=O)[O-]) `REAL300004918828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918828 none CC#CCC(NC(=O)C1=C(Cl)C2=CC=CC=C2N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 32, 32, 58, 58, 58, 58, 58, 21, 6, 1, 1, 1, 1, 2, 2, 2] 58 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918828 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918828 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918828/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918828 Building REAL300004918829 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918829' /scratch/stefan/7775246/working/building/REAL300004918829 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918829 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918829/0 /scratch/stefan/7775246/working/building/REAL300004918829 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/835 `/scratch/stefan/7775246/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C2=CC=CC=C2N1C)C(=O)[O-]) `REAL300004918829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918829 none CC#CCC(NC(=O)C1=C(Br)C2=CC=CC=C2N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 31, 31, 53, 53, 53, 53, 53, 21, 6, 1, 1, 1, 1, 2, 2, 2] 53 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918829 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918829 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918829/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918829 Building REAL300004918830 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918830' /scratch/stefan/7775246/working/building/REAL300004918830 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918830 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918830/0 /scratch/stefan/7775246/working/building/REAL300004918830 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/836 `/scratch/stefan/7775246/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC(CCC)=NO1)C(=O)[O-]) `REAL300004918830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918830 none CC#CCC(NC(=O)CCCC1=NC(CCC)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 65, 49, 49, 22, 49, 15, 7, 1, 1, 1, 1, 1, 9, 17, 1, 1, 65, 72, 72, 96, 96, 96, 96, 96, 65, 49, 22, 22, 15, 15, 7, 7, 9, 9, 17, 17, 17, 17, 17] 201 rigid atoms, others: [10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 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: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918830 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918830 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918830/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918830 Building REAL300004918831 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918831' /scratch/stefan/7775246/working/building/REAL300004918831 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918831 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918831/0 /scratch/stefan/7775246/working/building/REAL300004918831 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/837 `/scratch/stefan/7775246/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=CC2=CC(OC)=CC=C21)C(=O)[O-]) `REAL300004918831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918831 none CC#CCC(NC(=O)CN1C=CC2=CC(OC)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 73, 35, 35, 7, 35, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 73, 118, 118, 156, 156, 156, 156, 156, 73, 35, 7, 7, 1, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918831 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918831 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918831/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918831 Building REAL300004918832 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918832' /scratch/stefan/7775246/working/building/REAL300004918832 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918832 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918832/0 /scratch/stefan/7775246/working/building/REAL300004918832 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/838 `/scratch/stefan/7775246/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004918832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918832 none CC#CCC(NC(=O)CCCC1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 154, 114, 114, 34, 114, 16, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 154, 159, 159, 191, 191, 191, 191, 191, 154, 114, 34, 34, 16, 16, 8, 8, 1, 6, 6, 1, 6, 6] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 863 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918832 none CC#CCC(NC(=O)CCCC1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 187, 164, 164, 75, 164, 48, 27, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 187, 194, 194, 201, 201, 201, 201, 201, 187, 164, 75, 75, 48, 48, 27, 26, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918832 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918832 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918832/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918832 Building REAL300004918833 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918833' /scratch/stefan/7775246/working/building/REAL300004918833 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918833 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918833/0 /scratch/stefan/7775246/working/building/REAL300004918833 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/839 `/scratch/stefan/7775246/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(=O)C=C(C)C)C=C1)C(=O)[O-]) `REAL300004918833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918833 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)C=C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 18, 18, 18, 51, 51, 51, 1, 1, 7, 11, 11, 19, 19, 19, 19, 19, 7, 3, 1, 1, 6, 6, 18, 51, 51, 51, 51, 51, 51, 51, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918833 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918833 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918833/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918833 Building REAL300004918834 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918834' /scratch/stefan/7775246/working/building/REAL300004918834 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918834 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918834/0 /scratch/stefan/7775246/working/building/REAL300004918834 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/840 `/scratch/stefan/7775246/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNS(=O)(=O)CC)C=C1)C(=O)[O-]) `REAL300004918834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918834 none CC#CCC(NC(=O)C1=CC=C(CNS(=O)(=O)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 25, 44, 44, 44, 52, 1, 1, 7, 10, 10, 18, 18, 18, 18, 18, 7, 3, 1, 1, 6, 6, 25, 52, 52, 52, 52, 52, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 19, 20, 41, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918834 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918834 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918834/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918834 Building REAL300004918835 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918835' /scratch/stefan/7775246/working/building/REAL300004918835 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918835 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918835/0 /scratch/stefan/7775246/working/building/REAL300004918835 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/841 `/scratch/stefan/7775246/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=CC=C(C(C)C)C=C2)C1=O)C(=O)[O-]) `REAL300004918835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918835 none CC#CCC(NC(=O)C1CCN(C2=CC=C(C(C)C)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 1, 1, 11, 11, 6, 6, 1, 1, 37, 62, 62, 103, 103, 103, 103, 103, 37, 12, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 6, 6] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 540 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918835 none CC#CCC(NC(=O)C1CCN(C2=CC=C(C(C)C)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 85, 33, 33, 6, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 6, 6, 85, 125, 125, 160, 160, 160, 160, 160, 85, 33, 6, 6, 6, 6, 6, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [48, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 817 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918835 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918835 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918835/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918835 Building REAL300004918836 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918836' /scratch/stefan/7775246/working/building/REAL300004918836 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918836 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918836/0 /scratch/stefan/7775246/working/building/REAL300004918836 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/842 `/scratch/stefan/7775246/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)NCC(C)C)C1)C(=O)[O-]) `REAL300004918836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918836 none CC#CCC(NC(=O)C1CCCN(C(=O)NCC(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 20, 25, 1, 21, 32, 32, 49, 49, 49, 49, 49, 21, 9, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 25, 25, 25, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 48, 49, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 357 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918836 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918836 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918836/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918836 Building REAL300004918837 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918837' /scratch/stefan/7775246/working/building/REAL300004918837 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918837 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918837/0 /scratch/stefan/7775246/working/building/REAL300004918837 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/843 `/scratch/stefan/7775246/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNS(=O)(=O)C1=CC=C(C(=O)NC(CC#CC)C(=O)[O-])C=C1) `REAL300004918837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918837 none C=CCNS(=O)(=O)C1=CC=C(C(=O)NC(CC#CC)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.1', 'C.1', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 45, 45, 45, 15, 24, 24, 1, 1, 32, 32, 32, 15, 15, 5, 1, 1, 5, 15, 45, 45, 45, 45, 45, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 22, 23, 39, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918837 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918837 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918837/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918837 Building REAL300004918838 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918838' /scratch/stefan/7775246/working/building/REAL300004918838 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918838 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918838/0 /scratch/stefan/7775246/working/building/REAL300004918838 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/844 `/scratch/stefan/7775246/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=NC3=CC=CC=C3O2)CC1)C(=O)[O-]) `REAL300004918838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918838 none CC#CCC(NC(=O)C1CCN(C2=NC3=CC=CC=C3O2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 41, 13, 13, 1, 13, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 41, 49, 49, 70, 70, 70, 70, 70, 41, 13, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1] 134 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 45, 44, 43, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918838 none CC#CCC(NC(=O)C1CCN(C2=NC3=CC=CC=C3O2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 78, 25, 25, 2, 25, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 78, 93, 93, 134, 134, 134, 134, 134, 78, 25, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2] 134 rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918838 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918838 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918838/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918838 Building REAL300004918839 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918839' /scratch/stefan/7775246/working/building/REAL300004918839 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918839 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918839/0 /scratch/stefan/7775246/working/building/REAL300004918839 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/845 `/scratch/stefan/7775246/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-]) `REAL300004918839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918839 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 10, 1, 10, 1, 1, 1, 1, 7, 10, 10, 8, 10, 10, 1, 1, 1, 10, 10, 10, 10, 23, 35, 35, 40, 40, 40, 40, 40, 23, 10, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918839 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 51, 29, 29, 10, 29, 10, 10, 10, 10, 37, 52, 52, 44, 52, 52, 10, 1, 1, 1, 1, 1, 1, 51, 67, 67, 75, 75, 75, 75, 75, 51, 29, 10, 37, 37, 52, 52, 49, 52, 52, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918839 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 81, 45, 45, 10, 45, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 52, 52, 52, 81, 103, 103, 129, 129, 129, 129, 129, 81, 45, 10, 3, 3, 1, 1, 1, 1, 1, 52, 52, 52] 201 rigid atoms, others: [38, 39, 40, 41, 42, 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, 43, 44, 45]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918839 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918839 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918839/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918839 Building REAL300004918840 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918840' /scratch/stefan/7775246/working/building/REAL300004918840 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918840 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918840/0 /scratch/stefan/7775246/working/building/REAL300004918840 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/846 `/scratch/stefan/7775246/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCC2C)=C1)C(=O)[O-]) `REAL300004918840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918840 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCC2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 21, 30, 30, 50, 50, 50, 50, 50, 21, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 149 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 49, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 258 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918840 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCCCC2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 76, 27, 27, 7, 27, 7, 7, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 76, 103, 103, 149, 149, 149, 149, 149, 76, 27, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7] 149 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 13, 45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 728 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918840 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918840 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918840/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918840 Building REAL300004918841 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918841' /scratch/stefan/7775246/working/building/REAL300004918841 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918841 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918841/0 /scratch/stefan/7775246/working/building/REAL300004918841 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/847 `/scratch/stefan/7775246/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OCCC)C(OC)=C1)C(=O)[O-]) `REAL300004918841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918841 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OCCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 52, 29, 29, 5, 29, 5, 1, 1, 1, 1, 1, 1, 1, 3, 9, 17, 1, 1, 4, 1, 52, 52, 52, 76, 76, 76, 76, 76, 52, 29, 5, 5, 1, 9, 9, 21, 21, 21, 21, 21, 4, 4, 4, 1] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 46, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 460 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918841 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918841 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918841/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918841 Building REAL300004918842 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918842' /scratch/stefan/7775246/working/building/REAL300004918842 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918842 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918842/0 /scratch/stefan/7775246/working/building/REAL300004918842 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/848 `/scratch/stefan/7775246/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C3OCCOC3=C2)S1)C(=O)[O-]) `REAL300004918842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918842 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C3OCCOC3=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 12, 12, 13, 13, 13, 13, 13, 1, 28, 45, 45, 68, 68, 68, 68, 68, 28, 11, 1, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918842 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C3OCCOC3=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 69, 69, 13, 68, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 129, 157, 157, 201, 201, 201, 201, 201, 129, 69, 13, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918842 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918842 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918842/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918842 Building REAL300004918843 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918843' /scratch/stefan/7775246/working/building/REAL300004918843 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918843 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918843/0 /scratch/stefan/7775246/working/building/REAL300004918843 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/849 `/scratch/stefan/7775246/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004918843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918843 none CC#CCC(NC(=O)C=CC1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 71, 41, 41, 9, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 71, 94, 94, 135, 135, 135, 135, 135, 71, 41, 9, 9, 1, 1, 1, 1, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 716 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918843 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918843 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918843/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918843 Building REAL300004918844 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918844' /scratch/stefan/7775246/working/building/REAL300004918844 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918844 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918844/0 /scratch/stefan/7775246/working/building/REAL300004918844 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/850 `/scratch/stefan/7775246/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCCC2C)C=C1)C(=O)[O-]) `REAL300004918844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918844 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCCC2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 12, 16, 16, 29, 29, 29, 29, 29, 12, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 59 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 48, 49, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918844 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCCC2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 29, 12, 12, 3, 12, 4, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 40, 40, 59, 59, 59, 59, 59, 29, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7] 59 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 15, 16, 17, 18, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 315 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918844 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918844 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918844/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918844 Building REAL300004918845 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918845' /scratch/stefan/7775246/working/building/REAL300004918845 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918845 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918845/0 /scratch/stefan/7775246/working/building/REAL300004918845 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/851 `/scratch/stefan/7775246/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCC(C)C)=C1)C(=O)[O-]) `REAL300004918845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918845 none CC#CCC(NC(=O)C1=CC=CC(OCC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 9, 14, 14, 1, 13, 25, 25, 43, 43, 43, 43, 43, 13, 5, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 18, 41, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918845 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918845 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918845/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918845 Building REAL300004918846 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918846' /scratch/stefan/7775246/working/building/REAL300004918846 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918846 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918846/0 /scratch/stefan/7775246/working/building/REAL300004918846 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/852 `/scratch/stefan/7775246/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004918846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918846 none CC#CCC(NC(=O)C(C)OC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 88, 88, 20, 88, 8, 20, 1, 1, 1, 1, 1, 1, 1, 1, 131, 158, 158, 201, 201, 201, 201, 201, 131, 88, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 955 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918846 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918846 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918846/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918846 Building REAL300004918847 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918847' /scratch/stefan/7775246/working/building/REAL300004918847 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918847 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918847/0 /scratch/stefan/7775246/working/building/REAL300004918847 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/853 `/scratch/stefan/7775246/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004918847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918847 none CC#CCC(NC(=O)C=CC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 124, 61, 61, 9, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 124, 149, 149, 199, 199, 199, 199, 199, 124, 61, 9, 9, 1, 1, 1, 1] 199 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 875 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918847 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918847 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918847/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918847 Building REAL300004918848 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918848' /scratch/stefan/7775246/working/building/REAL300004918848 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918848 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918848/0 /scratch/stefan/7775246/working/building/REAL300004918848 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/854 `/scratch/stefan/7775246/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918848 none CC#CCC(NC(=O)CCSC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 89, 89, 21, 89, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 128, 173, 173, 201, 201, 201, 201, 201, 128, 89, 21, 21, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 982 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918848 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918848 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918848/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918848 Building REAL300004918849 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918849' /scratch/stefan/7775246/working/building/REAL300004918849 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918849 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918849/0 /scratch/stefan/7775246/working/building/REAL300004918849 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/855 `/scratch/stefan/7775246/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004918849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918849 none CC#CCC(NC(=O)CC(C)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 25, 25, 6, 25, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 41, 25, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918849 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918849 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918849/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918849 Building REAL300004918850 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918850' /scratch/stefan/7775246/working/building/REAL300004918850 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918850 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918850/0 /scratch/stefan/7775246/working/building/REAL300004918850 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/856 `/scratch/stefan/7775246/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C(NC(C)=O)=C1)C(=O)[O-]) `REAL300004918850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918850 none CC#CCC(NC(=O)C1=CC=C(F)C(NC(C)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 1, 5, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 31, 47, 47, 99, 99, 99, 99, 99, 31, 7, 1, 1, 4, 4, 4, 4, 1] 186 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 13, 14, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918850 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918850 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918850/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918850 Building REAL300004918851 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918851' /scratch/stefan/7775246/working/building/REAL300004918851 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918851 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918851/0 /scratch/stefan/7775246/working/building/REAL300004918851 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/857 `/scratch/stefan/7775246/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)CC)C=C1)C(=O)[O-]) `REAL300004918851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918851 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 15, 1, 1, 16, 26, 26, 52, 52, 52, 52, 52, 16, 4, 1, 1, 15, 15, 16, 16, 16, 1, 1] 162 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918851 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918851 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918851/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918851 Building REAL300004918852 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918852' /scratch/stefan/7775246/working/building/REAL300004918852 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918852 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918852/0 /scratch/stefan/7775246/working/building/REAL300004918852 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/858 `/scratch/stefan/7775246/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(O)(C1=NC(C)=CS1)C(F)(F)F)C(=O)[O-]) `REAL300004918852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918852 none CC#CCC(NC(=O)CC(O)(C1=NC(C)=CS1)C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 1, 5, 1, 14, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 14, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 14, 14, 14, 16, 16, 16, 16, 16, 14, 13, 13, 13, 27, 2, 2, 2, 1] 48 rigid atoms, others: [37, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918852 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918852 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918852/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918852 Building REAL300004918853 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918853' /scratch/stefan/7775246/working/building/REAL300004918853 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918853 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918853/0 /scratch/stefan/7775246/working/building/REAL300004918853 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/859 `/scratch/stefan/7775246/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004918853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918853 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 31, 30, 30, 15, 30, 10, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 36, 36, 36, 36, 36, 31, 30, 15, 15, 10, 10, 5, 1, 1, 1, 1] 36 rigid atoms, others: [38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918853 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918853 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918853/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918853 Building REAL300004918854 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918854' /scratch/stefan/7775246/working/building/REAL300004918854 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918854 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918854/0 /scratch/stefan/7775246/working/building/REAL300004918854 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/860 `/scratch/stefan/7775246/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004918854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918854 none CC#CCC(NC(=O)CSCC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 159, 159, 69, 159, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 185, 187, 187, 201, 201, 201, 201, 201, 185, 159, 69, 69, 4, 4, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918854 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918854 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918854/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918854 Building REAL300004918855 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918855' /scratch/stefan/7775246/working/building/REAL300004918855 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918855 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918855/0 /scratch/stefan/7775246/working/building/REAL300004918855 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/861 `/scratch/stefan/7775246/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004918855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918855 none CC#CCC(NC(=O)CCCCC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 99, 63, 63, 16, 63, 7, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 100, 101, 101, 113, 113, 113, 113, 113, 100, 63, 16, 16, 7, 7, 5, 5, 3, 3, 1, 1, 2, 2, 2, 1, 1] 113 rigid atoms, others: [43, 37, 38, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 484 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918855 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918855 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918855/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918855 Building REAL300004918856 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918856' /scratch/stefan/7775246/working/building/REAL300004918856 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918856 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918856/0 /scratch/stefan/7775246/working/building/REAL300004918856 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/862 `/scratch/stefan/7775246/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCOC1=CC(C)=CC=C1C)C(=O)[O-]) `REAL300004918856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918856 none CC#CCC(NC(=O)CCCCOC1=CC(C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 170, 170, 65, 170, 40, 38, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 65, 65, 40, 40, 40, 40, 23, 23, 1, 2, 2, 2, 1, 1, 2, 2, 2] 201 rigid atoms, others: [39, 44, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 45, 46, 47]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918856 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918856 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918856/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918856 Building REAL300004918857 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918857' /scratch/stefan/7775246/working/building/REAL300004918857 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918857 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918857/0 /scratch/stefan/7775246/working/building/REAL300004918857 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/863 `/scratch/stefan/7775246/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCOC1=CC=CC(C)=C1)C(=O)[O-]) `REAL300004918857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918857 none CC#CCC(NC(=O)CCCCOC1=CC=CC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 165, 132, 132, 47, 132, 24, 24, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 165, 172, 172, 201, 201, 201, 201, 201, 165, 132, 47, 47, 24, 24, 24, 24, 10, 10, 1, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [38, 39, 40, 44, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 880 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918857 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918857 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918857/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918857 Building REAL300004918858 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918858' /scratch/stefan/7775246/working/building/REAL300004918858 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918858 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918858/0 /scratch/stefan/7775246/working/building/REAL300004918858 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/864 `/scratch/stefan/7775246/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OC(C)C)=C1)C(=O)[O-]) `REAL300004918858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918858 none CC#CCC(NC(=O)CC1=CC=CC(OC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 37, 16, 16, 6, 16, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 37, 54, 54, 81, 81, 81, 81, 81, 37, 16, 6, 6, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 18, 41, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 445 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918858 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918858 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918858/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918858 Building REAL300004918859 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918859' /scratch/stefan/7775246/working/building/REAL300004918859 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918859 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918859/0 /scratch/stefan/7775246/working/building/REAL300004918859 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/865 `/scratch/stefan/7775246/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C(C2CC2)=NN1)C(=O)[O-]) `REAL300004918859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918859 none CC#CCC(NC(=O)C1=C(Br)C(C2CC2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 5, 5, 5, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 8, 1, 1, 27, 42, 42, 86, 86, 86, 86, 86, 27, 7, 8, 8, 8, 8, 8, 1] 173 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918859 none CC#CCC(NC(=O)C1=C(Br)C(C2CC2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 5, 5, 5, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 104, 36, 36, 8, 36, 8, 8, 9, 1, 1, 1, 1, 8, 8, 104, 132, 132, 173, 173, 173, 173, 173, 104, 36, 1, 1, 1, 1, 1, 8] 173 rigid atoms, others: [11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918859 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918859 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918859/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918859 Building REAL300004918860 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918860' /scratch/stefan/7775246/working/building/REAL300004918860 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918860 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918860/0 /scratch/stefan/7775246/working/building/REAL300004918860 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/866 `/scratch/stefan/7775246/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004918860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918860 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 14, 21, 21, 41, 41, 41, 41, 41, 14, 6, 1, 7, 7, 2, 7, 7, 1] 55 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918860 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 15, 15, 1, 15, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 41, 41, 55, 55, 55, 55, 55, 35, 15, 7, 1, 1, 1, 1, 1, 7] 55 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918860 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918860 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918860/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918860 Building REAL300004918861 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918861' /scratch/stefan/7775246/working/building/REAL300004918861 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918861 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918861/0 /scratch/stefan/7775246/working/building/REAL300004918861 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/867 `/scratch/stefan/7775246/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC=C2OC)C=C1)C(=O)[O-]) `REAL300004918861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918861 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC=C2OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 37, 11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 9, 8, 9, 9, 9, 11, 1, 1, 37, 55, 55, 93, 93, 93, 93, 93, 37, 11, 9, 9, 9, 9, 8, 9, 11, 11, 11, 1, 1] 193 rigid atoms, others: [6, 8, 9, 10, 11, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918861 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC=C2OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 83, 34, 34, 9, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 83, 121, 121, 172, 172, 172, 172, 172, 83, 34, 1, 2, 2, 2, 1, 1, 4, 4, 4, 9, 9] 193 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918861 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918861 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918861/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918861 Building REAL300004918862 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918862' /scratch/stefan/7775246/working/building/REAL300004918862 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918862 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918862/0 /scratch/stefan/7775246/working/building/REAL300004918862 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/868 `/scratch/stefan/7775246/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2C)C2=C1CCC2)C(=O)[O-]) `REAL300004918862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918862 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2C)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 36, 12, 12, 1, 12, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 36, 49, 49, 79, 79, 79, 79, 79, 36, 12, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 194 rigid atoms, others: [43, 6, 8, 9, 10, 11, 44, 45, 40, 18, 19, 20, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918862 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2C)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 111, 51, 51, 8, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 111, 140, 140, 194, 194, 194, 194, 194, 111, 51, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8] 194 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918862 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918862 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918862/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918862 Building REAL300004918863 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918863' /scratch/stefan/7775246/working/building/REAL300004918863 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918863 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918863/0 /scratch/stefan/7775246/working/building/REAL300004918863 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/869 `/scratch/stefan/7775246/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CN(CC2=CC=CC=C2)C1=O)C(=O)[O-]) `REAL300004918863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918863 none CC#CCC(NC(=O)C1=CC=CN(CC2=CC=CC=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 32, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 4, 12, 12, 6, 12, 12, 1, 1, 32, 50, 50, 78, 78, 78, 78, 78, 32, 13, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918863 none CC#CCC(NC(=O)C1=CC=CN(CC2=CC=CC=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 64, 64, 12, 64, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 117, 155, 155, 201, 201, 201, 201, 201, 117, 64, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 962 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918863 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918863 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918863/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918863 Building REAL300004918864 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918864' /scratch/stefan/7775246/working/building/REAL300004918864 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918864 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918864/0 /scratch/stefan/7775246/working/building/REAL300004918864 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/870 `/scratch/stefan/7775246/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC2=CC(Cl)=CC=C2S1)C(=O)[O-]) `REAL300004918864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918864 none CC#CCC(NC(=O)CCC1=NC2=CC(Cl)=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 16, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 67, 41, 41, 13, 41, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 76, 76, 88, 88, 88, 88, 88, 67, 41, 13, 13, 5, 5, 1, 1, 1] 88 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918864 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918864 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918864/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918864 Building REAL300004918865 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918865' /scratch/stefan/7775246/working/building/REAL300004918865 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918865 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918865/0 /scratch/stefan/7775246/working/building/REAL300004918865 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/871 `/scratch/stefan/7775246/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)CC1CCCCC1)C(=O)[O-]) `REAL300004918865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918865 none CC#CCC(NC(=O)CNC(=O)CC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 96, 96, 47, 96, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 135, 172, 172, 201, 201, 201, 201, 201, 135, 96, 47, 47, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1036 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918865 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918865 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918865/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918865 Building REAL300004918866 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918866' /scratch/stefan/7775246/working/building/REAL300004918866 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918866 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918866/0 /scratch/stefan/7775246/working/building/REAL300004918866 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/872 `/scratch/stefan/7775246/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC(=O)CC1CCCCC1)C(=O)[O-]) `REAL300004918866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918866 none CC#CCC(NC(=O)C(C)NC(=O)CC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 123, 81, 81, 39, 81, 24, 39, 24, 5, 24, 1, 1, 1, 1, 1, 1, 1, 123, 165, 165, 201, 201, 201, 201, 201, 123, 81, 39, 39, 39, 39, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1058 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918866 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918866 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918866/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918866 Building REAL300004918867 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918867' /scratch/stefan/7775246/working/building/REAL300004918867 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918867 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918867/0 /scratch/stefan/7775246/working/building/REAL300004918867 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/873 `/scratch/stefan/7775246/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)NC(=O)C1CCCC1)C(=O)[O-]) `REAL300004918867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918867 none CC#CCC(NC(=O)CC(C)NC(=O)C1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 36, 28, 28, 13, 28, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 36, 36, 36, 44, 44, 44, 44, 44, 36, 28, 13, 13, 10, 10, 10, 10, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 44 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918867 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918867 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918867/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918867 Building REAL300004918868 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918868' /scratch/stefan/7775246/working/building/REAL300004918868 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918868 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918868/0 /scratch/stefan/7775246/working/building/REAL300004918868 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/874 `/scratch/stefan/7775246/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)N1C)C(=O)[O-]) `REAL300004918868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918868 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 42, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 42, 64, 64, 104, 104, 104, 104, 104, 42, 12, 1, 1, 4, 4, 4, 4, 2, 2, 2] 112 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 522 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918868 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(F)C=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 75, 31, 31, 4, 31, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 75, 91, 91, 112, 112, 112, 112, 112, 75, 31, 4, 4, 1, 1, 1, 1, 4, 4, 4] 112 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 513 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918868 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918868 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918868/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918868 Building REAL300004918869 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918869' /scratch/stefan/7775246/working/building/REAL300004918869 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918869 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918869/0 /scratch/stefan/7775246/working/building/REAL300004918869 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/875 `/scratch/stefan/7775246/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC(C)=C2)N=N1)C(=O)[O-]) `REAL300004918869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918869 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(C)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 43, 13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 43, 68, 68, 103, 103, 103, 103, 103, 43, 13, 1, 7, 7, 3, 7, 7, 7, 7] 173 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918869 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(C)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 101, 47, 47, 7, 47, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 101, 131, 131, 173, 173, 173, 173, 173, 101, 47, 7, 1, 1, 1, 2, 2, 2, 1] 173 rigid atoms, others: [32, 33, 37, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 820 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918869 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918869 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918869/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918869 Building REAL300004918870 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918870' /scratch/stefan/7775246/working/building/REAL300004918870 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918870 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918870/0 /scratch/stefan/7775246/working/building/REAL300004918870 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/876 `/scratch/stefan/7775246/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)CC(C)(C)C)C(=O)[O-]) `REAL300004918870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918870 none CC#CCC(NC(=O)C1CCCN1C(=O)CC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 10, 13, 13, 13, 22, 36, 36, 53, 53, 53, 53, 53, 22, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13] 110 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 319 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918870 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918870 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918870/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918870 Building REAL300004918871 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918871' /scratch/stefan/7775246/working/building/REAL300004918871 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918871 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918871/0 /scratch/stefan/7775246/working/building/REAL300004918871 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/877 `/scratch/stefan/7775246/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C2OCCOC2=C1)C(=O)[O-]) `REAL300004918871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918871 none CC#CCC(NC(=O)C(C)(C)C1=CC=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 54, 54, 13, 54, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 147, 147, 201, 201, 201, 201, 201, 109, 54, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 37, 38, 39, 8, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 997 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918871 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918871 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918871/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918871 Building REAL300004918872 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918872' /scratch/stefan/7775246/working/building/REAL300004918872 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918872 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918872/0 /scratch/stefan/7775246/working/building/REAL300004918872 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/878 `/scratch/stefan/7775246/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC([N+](=O)[O-])=C2)=N1)C(=O)[O-]) `REAL300004918872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918872 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC([N+](=O)[O-])=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 1, 37, 55, 55, 88, 88, 88, 88, 88, 37, 11, 1, 5, 5, 2, 5] 149 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918872 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC([N+](=O)[O-])=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 82, 35, 35, 5, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 82, 109, 109, 149, 149, 149, 149, 149, 82, 35, 5, 1, 1, 1, 1] 149 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918872 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918872 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918872/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918872 Building REAL300004918873 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918873' /scratch/stefan/7775246/working/building/REAL300004918873 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918873 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918873/0 /scratch/stefan/7775246/working/building/REAL300004918873 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/879 `/scratch/stefan/7775246/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=C(Cl)C=C2Cl)=N1)C(=O)[O-]) `REAL300004918873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918873 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(Cl)C=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 52, 29, 29, 6, 29, 1, 1, 1, 1, 1, 1, 8, 8, 2, 8, 8, 8, 8, 1, 52, 84, 84, 106, 106, 106, 106, 106, 52, 29, 6, 6, 1, 8, 8, 8] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918873 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(Cl)C=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 92, 92, 27, 92, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 133, 160, 160, 201, 201, 201, 201, 201, 133, 92, 27, 27, 8, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 948 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918873 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918873 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918873/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918873 Building REAL300004918874 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918874' /scratch/stefan/7775246/working/building/REAL300004918874 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918874 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918874/0 /scratch/stefan/7775246/working/building/REAL300004918874 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/880 `/scratch/stefan/7775246/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C(C)(C)C)S1)C(=O)[O-]) `REAL300004918874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918874 none CC#CCC(NC(=O)C1=C(C)N=C(C(C)(C)C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 33, 47, 47, 72, 72, 72, 72, 72, 33, 11, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 117 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 17] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 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: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918874 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918874 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918874/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918874 Building REAL300004918875 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918875' /scratch/stefan/7775246/working/building/REAL300004918875 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918875 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918875/0 /scratch/stefan/7775246/working/building/REAL300004918875 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/881 `/scratch/stefan/7775246/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=C(C)C=C2C)S1)C(=O)[O-]) `REAL300004918875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918875 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C(C)C=C2C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 35, 13, 13, 1, 13, 1, 1, 1, 1, 1, 10, 10, 1, 9, 10, 10, 10, 1, 35, 58, 58, 91, 91, 91, 91, 91, 35, 13, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918875 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C(C)C=C2C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 76, 76, 10, 76, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 135, 163, 163, 201, 201, 201, 201, 201, 135, 76, 10, 1, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40]) total number of confs: 891 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918875 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918875 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918875/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918875 Building REAL300004918876 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918876' /scratch/stefan/7775246/working/building/REAL300004918876 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918876 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918876/0 /scratch/stefan/7775246/working/building/REAL300004918876 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/882 `/scratch/stefan/7775246/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)NC(=O)N2C1CCCC1)C(=O)[O-]) `REAL300004918876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918876 none CC#CCC(NC(=O)C1=CC=C2C(=C1)NC(=O)N2C1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 31, 45, 45, 71, 71, 71, 71, 71, 31, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] 144 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 343 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918876 none CC#CCC(NC(=O)C1=CC=C2C(=C1)NC(=O)N2C1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 69, 24, 24, 7, 24, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 69, 98, 98, 144, 144, 144, 144, 144, 69, 24, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 144 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 699 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918876 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918876 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918876/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918876 Building REAL300004918877 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918877' /scratch/stefan/7775246/working/building/REAL300004918877 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918877 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918877/0 /scratch/stefan/7775246/working/building/REAL300004918877 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/883 `/scratch/stefan/7775246/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC(Cl)=CC=C12)C(=O)[O-]) `REAL300004918877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918877 none CC#CCC(NC(=O)CC1=CNC2=CC(Cl)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 95, 49, 49, 8, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 135, 135, 201, 201, 201, 201, 201, 95, 49, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 989 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918877 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918877 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918877/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918877 Building REAL300004918878 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918878' /scratch/stefan/7775246/working/building/REAL300004918878 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918878 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918878/0 /scratch/stefan/7775246/working/building/REAL300004918878 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/884 `/scratch/stefan/7775246/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(Cl)=CC=C1Cl)C(=O)[O-]) `REAL300004918878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918878 none CC#CCC(NC(=O)CC1=CC(Cl)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 94, 39, 39, 6, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 138, 138, 201, 201, 201, 201, 201, 94, 39, 6, 6, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 997 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918878 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918878 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918878/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918878 Building REAL300004918879 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918879' /scratch/stefan/7775246/working/building/REAL300004918879 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918879 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918879/0 /scratch/stefan/7775246/working/building/REAL300004918879 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/885 `/scratch/stefan/7775246/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004918879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918879 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 40, 12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 40, 60, 60, 87, 87, 87, 87, 87, 40, 12, 1, 3, 3, 1, 3, 3, 2, 2, 2] 94 rigid atoms, others: [6, 8, 9, 10, 11, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 445 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918879 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 57, 24, 24, 3, 23, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 57, 70, 70, 94, 94, 94, 94, 94, 57, 24, 3, 1, 1, 1, 1, 1, 4, 4, 4] 94 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 427 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918879 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918879 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918879/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918879 Building REAL300004918880 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918880' /scratch/stefan/7775246/working/building/REAL300004918880 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918880 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918880/0 /scratch/stefan/7775246/working/building/REAL300004918880 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/886 `/scratch/stefan/7775246/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=C(Cl)C=CC=C2Cl)C(CC)=N1)C(=O)[O-]) `REAL300004918880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918880 none CC#CCC(NC(=O)C1=NN(C2=C(Cl)C=CC=C2Cl)C(CC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 37, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 3, 4, 4, 4, 1, 1, 6, 1, 37, 60, 60, 114, 114, 114, 114, 114, 37, 12, 4, 3, 4, 6, 6, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918880 none CC#CCC(NC(=O)C1=NN(C2=C(Cl)C=CC=C2Cl)C(CC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 92, 34, 34, 5, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 5, 92, 135, 135, 167, 167, 167, 167, 167, 92, 34, 1, 1, 1, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 892 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918880 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918880 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918880/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918880 Building REAL300004918881 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918881' /scratch/stefan/7775246/working/building/REAL300004918881 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918881 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918881/0 /scratch/stefan/7775246/working/building/REAL300004918881 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/887 `/scratch/stefan/7775246/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C([N+](=O)[O-])C=C2)=N1)C(=O)[O-]) `REAL300004918881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918881 none CC#CCC(NC(=O)C1=CSC(C2=CC=C([N+](=O)[O-])C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 3, 3, 1, 37, 56, 56, 86, 86, 86, 86, 86, 37, 12, 1, 3, 3, 3, 3] 93 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918881 none CC#CCC(NC(=O)C1=CSC(C2=CC=C([N+](=O)[O-])C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 59, 28, 28, 3, 28, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 59, 71, 71, 93, 93, 93, 93, 93, 59, 29, 3, 1, 1, 1, 1] 93 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918881 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918881 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918881/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918881 Building REAL300004918882 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918882' /scratch/stefan/7775246/working/building/REAL300004918882 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918882 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918882/0 /scratch/stefan/7775246/working/building/REAL300004918882 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/888 `/scratch/stefan/7775246/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(C2=CC=C(OC)C=C2F)=C1)C(=O)[O-]) `REAL300004918882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918882 none CC#CCC(NC(=O)C1=NOC(C2=CC=C(OC)C=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 1, 12, 25, 13, 13, 13, 1, 17, 27, 27, 44, 44, 44, 44, 44, 17, 6, 13, 13, 25, 25, 25, 13, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918882 none CC#CCC(NC(=O)C1=NOC(C2=CC=C(OC)C=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 99, 46, 46, 13, 46, 13, 13, 13, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 13, 99, 132, 132, 175, 175, 175, 175, 175, 99, 46, 1, 1, 3, 3, 3, 1, 13] 201 rigid atoms, others: [32, 33, 37, 11, 12, 13, 14, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38]) total number of confs: 850 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918882 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918882 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918882/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918882 Building REAL300004918883 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918883' /scratch/stefan/7775246/working/building/REAL300004918883 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918883 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918883/0 /scratch/stefan/7775246/working/building/REAL300004918883 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/889 `/scratch/stefan/7775246/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004918883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918883 none CC#CCC(NC(=O)CCCOC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 132, 102, 102, 45, 102, 38, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 132, 158, 158, 201, 201, 201, 201, 201, 132, 102, 45, 45, 38, 38, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1008 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918883 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918883 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918883/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918883 Building REAL300004918884 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918884' /scratch/stefan/7775246/working/building/REAL300004918884 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918884 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918884/0 /scratch/stefan/7775246/working/building/REAL300004918884 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/890 `/scratch/stefan/7775246/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CS(C)(=O)=O)O1)C(=O)[O-]) `REAL300004918884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918884 none CC#CCC(NC(=O)C1=CC=C(CS(C)(=O)=O)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 11, 11, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 14, 6, 7, 1, 7, 1, 1, 1, 1, 1, 5, 20, 20, 20, 1, 14, 23, 23, 35, 35, 35, 35, 35, 14, 7, 1, 1, 5, 5, 21, 21, 21] 129 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918884 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918884 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918884/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918884 Building REAL300004918885 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918885' /scratch/stefan/7775246/working/building/REAL300004918885 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918885 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918885/0 /scratch/stefan/7775246/working/building/REAL300004918885 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/891 `/scratch/stefan/7775246/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(OC1CCCC1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918885 none CC#CCC(NC(=O)C(OC1CCCC1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 104, 61, 61, 17, 61, 6, 1, 1, 1, 1, 1, 1, 17, 32, 32, 20, 32, 32, 104, 140, 140, 185, 185, 185, 185, 185, 104, 61, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45]) total number of confs: 985 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918885 none CC#CCC(NC(=O)C(OC1CCCC1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 94, 40, 19, 19, 4, 19, 1, 4, 11, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 40, 62, 62, 94, 94, 94, 94, 94, 40, 19, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918885 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918885 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918885/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918885 Building REAL300004918886 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918886' /scratch/stefan/7775246/working/building/REAL300004918886 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918886 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918886/0 /scratch/stefan/7775246/working/building/REAL300004918886 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/892 `/scratch/stefan/7775246/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(CC)=N1)C(=O)[O-]) `REAL300004918886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918886 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(CC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 19, 6, 6, 1, 6, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 6, 1, 19, 33, 33, 59, 59, 59, 59, 59, 19, 6, 7, 7, 2, 7, 6, 6, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918886 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(CC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 81, 37, 37, 7, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 7, 81, 125, 125, 184, 184, 184, 184, 184, 81, 37, 1, 1, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 991 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918886 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918886 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918886/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918886 Building REAL300004918887 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918887' /scratch/stefan/7775246/working/building/REAL300004918887 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918887 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918887/0 /scratch/stefan/7775246/working/building/REAL300004918887 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/893 `/scratch/stefan/7775246/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C2CC2)=N1)C(=O)[O-]) `REAL300004918887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918887 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C2CC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 20, 6, 6, 1, 6, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 8, 8, 1, 20, 33, 33, 53, 53, 53, 53, 53, 20, 6, 7, 7, 2, 7, 8, 8, 8, 8, 8] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918887 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C2CC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 87, 41, 41, 8, 41, 8, 8, 8, 8, 27, 27, 15, 27, 27, 27, 1, 1, 1, 1, 8, 87, 125, 125, 162, 162, 162, 162, 162, 87, 41, 27, 27, 15, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 35, 36]) total number of confs: 870 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918887 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C2CC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 73, 35, 35, 7, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 7, 73, 106, 106, 153, 153, 153, 153, 153, 73, 35, 1, 1, 1, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 800 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918887 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918887 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918887/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918887 Building REAL300004918888 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918888' /scratch/stefan/7775246/working/building/REAL300004918888 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918888 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918888/0 /scratch/stefan/7775246/working/building/REAL300004918888 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/894 `/scratch/stefan/7775246/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2C(C)C)C(C)=N1)C(=O)[O-]) `REAL300004918888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918888 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2C(C)C)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 40, 12, 12, 1, 12, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 5, 1, 1, 1, 40, 65, 65, 108, 108, 108, 108, 108, 40, 12, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918888 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2C(C)C)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 42, 42, 5, 42, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 112, 145, 145, 201, 201, 201, 201, 201, 112, 42, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 949 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918888 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918888 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918888/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918888 Building REAL300004918889 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918889' /scratch/stefan/7775246/working/building/REAL300004918889 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918889 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918889/0 /scratch/stefan/7775246/working/building/REAL300004918889 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/895 `/scratch/stefan/7775246/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004918889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918889 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 50, 50, 13, 50, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 109, 145, 145, 201, 201, 201, 201, 201, 109, 50, 13, 13, 13, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 982 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918889 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918889 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918889/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918889 Building REAL300004918890 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918890' /scratch/stefan/7775246/working/building/REAL300004918890 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918890 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918890/0 /scratch/stefan/7775246/working/building/REAL300004918890 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/896 `/scratch/stefan/7775246/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918890 none CC#CCC(NC(=O)CSCC(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 178, 156, 156, 126, 156, 91, 39, 6, 1, 6, 1, 1, 1, 1, 1, 1, 178, 188, 188, 201, 201, 201, 201, 201, 178, 156, 126, 126, 39, 39, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918890 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918890 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918890/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918890 Building REAL300004918891 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918891' /scratch/stefan/7775246/working/building/REAL300004918891 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918891 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918891/0 /scratch/stefan/7775246/working/building/REAL300004918891 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/897 `/scratch/stefan/7775246/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CN(CC)C2=CC=CC=C12)C(=O)[O-]) `REAL300004918891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918891 none CC#CCC(NC(=O)CC1=CN(CC)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 50, 33, 33, 8, 33, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 50, 73, 73, 109, 109, 109, 109, 109, 50, 33, 8, 8, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918891 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918891 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918891/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918891 Building REAL300004918892 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918892' /scratch/stefan/7775246/working/building/REAL300004918892 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918892 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918892/0 /scratch/stefan/7775246/working/building/REAL300004918892 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/898 `/scratch/stefan/7775246/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C(=O)NCCC)=C1)C(=O)[O-]) `REAL300004918892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918892 none CC#CCC(NC(=O)C1=CC=CC(C(=O)NCCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 16, 1, 13, 20, 20, 41, 41, 41, 41, 41, 13, 5, 1, 1, 1, 3, 12, 12, 20, 20, 20, 20, 20, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918892 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918892 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918892/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918892 Building REAL300004918893 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918893' /scratch/stefan/7775246/working/building/REAL300004918893 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918893 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918893/0 /scratch/stefan/7775246/working/building/REAL300004918893 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/899 `/scratch/stefan/7775246/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCCCOC)=C1)C(=O)[O-]) `REAL300004918893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918893 none CC#CCC(NC(=O)C1=CC=CC(OCCCOC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 8, 16, 26, 30, 1, 11, 16, 16, 27, 27, 27, 27, 27, 11, 5, 1, 1, 1, 8, 8, 16, 16, 26, 26, 30, 30, 30, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 19, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918893 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918893 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918893/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918893 Building REAL300004918894 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918894' /scratch/stefan/7775246/working/building/REAL300004918894 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918894 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918894/0 /scratch/stefan/7775246/working/building/REAL300004918894 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/900 `/scratch/stefan/7775246/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CC2CC(=O)NC2=O)C=C1)C(=O)[O-]) `REAL300004918894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918894 none CC#CCC(NC(=O)C1=CC=C(CC2CC(=O)NC2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 1, 1, 13, 21, 21, 46, 46, 46, 46, 46, 13, 4, 1, 1, 7, 7, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 40, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 248 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918894 none CC#CCC(NC(=O)C1=CC=C(CC2CC(=O)NC2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 89, 32, 32, 16, 32, 11, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 89, 121, 121, 201, 201, 201, 201, 201, 89, 32, 16, 16, 6, 6, 1, 1, 1, 1, 16, 16] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 979 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918894 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918894 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918894/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918894 Building REAL300004918895 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918895' /scratch/stefan/7775246/working/building/REAL300004918895 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918895 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918895/0 /scratch/stefan/7775246/working/building/REAL300004918895 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/901 `/scratch/stefan/7775246/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CNC2=C(C)C=CC=C12)C(=O)[O-]) `REAL300004918895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918895 none CC#CCC(NC(=O)CCC1=CNC2=C(C)C=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 60, 41, 41, 11, 41, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 61, 61, 81, 81, 81, 81, 81, 60, 41, 11, 11, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1] 81 rigid atoms, others: [34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918895 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918895 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918895/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918895 Building REAL300004918896 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918896' /scratch/stefan/7775246/working/building/REAL300004918896 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918896 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918896/0 /scratch/stefan/7775246/working/building/REAL300004918896 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/902 `/scratch/stefan/7775246/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=CC(Cl)=CC(Cl)=C1)C(=O)[O-]) `REAL300004918896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918896 none CC#CCC(NC(=O)C1CC1C1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 30, 9, 9, 1, 9, 1, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 30, 49, 49, 86, 86, 86, 86, 86, 30, 9, 1, 1, 1, 1, 4, 2, 4] 111 rigid atoms, others: [32, 6, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 424 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918896 none CC#CCC(NC(=O)C1CC1C1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 48, 19, 19, 5, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 68, 68, 110, 110, 110, 110, 110, 48, 19, 5, 5, 5, 5, 1, 1, 1] 110 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 530 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918896 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918896 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918896/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918896 Building REAL300004918897 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918897' /scratch/stefan/7775246/working/building/REAL300004918897 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918897 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918897/0 /scratch/stefan/7775246/working/building/REAL300004918897 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/903 `/scratch/stefan/7775246/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(N2CCNC2=O)=CC=C1Cl)C(=O)[O-]) `REAL300004918897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918897 none CC#CCC(NC(=O)C1=CC(N2CCNC2=O)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 28, 7, 7, 1, 7, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 28, 42, 42, 71, 71, 71, 71, 71, 28, 7, 1, 9, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 17, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918897 none CC#CCC(NC(=O)C1=CC(N2CCNC2=O)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 89, 40, 40, 9, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 89, 130, 130, 201, 201, 201, 201, 201, 89, 40, 9, 1, 1, 1, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 963 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918897 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918897 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918897/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918897 Building REAL300004918898 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918898' /scratch/stefan/7775246/working/building/REAL300004918898 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918898 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918898/0 /scratch/stefan/7775246/working/building/REAL300004918898 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/904 `/scratch/stefan/7775246/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C(N2CCNC2=O)=C1)C(=O)[O-]) `REAL300004918898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918898 none CC#CCC(NC(=O)C1=CC=C(Cl)C(N2CCNC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 5, 5, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 17, 32, 32, 60, 60, 60, 60, 60, 17, 5, 1, 1, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [32, 38, 6, 8, 9, 10, 11, 12, 13, 14, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918898 none CC#CCC(NC(=O)C1=CC=C(Cl)C(N2CCNC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 5, 5, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 83, 25, 25, 6, 25, 6, 6, 6, 6, 7, 1, 1, 1, 1, 1, 1, 1, 6, 83, 113, 113, 201, 201, 201, 201, 201, 83, 25, 6, 6, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 920 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918898 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918898 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918898/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918898 Building REAL300004918899 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918899' /scratch/stefan/7775246/working/building/REAL300004918899 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918899 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918899/0 /scratch/stefan/7775246/working/building/REAL300004918899 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/905 `/scratch/stefan/7775246/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(CC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918899 none CC#CCC(NC(=O)CC(CC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 33, 21, 21, 7, 21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 33, 33, 33, 39, 39, 39, 39, 39, 33, 21, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 39 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918899 none CC#CCC(NC(=O)CC(CC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 32, 19, 19, 6, 19, 3, 1, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 32, 32, 32, 39, 39, 39, 39, 39, 32, 19, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 39 rigid atoms, others: [9, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918899 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918899 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918899/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918899 Building REAL300004918900 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918900' /scratch/stefan/7775246/working/building/REAL300004918900 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918900 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918900/0 /scratch/stefan/7775246/working/building/REAL300004918900 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/906 `/scratch/stefan/7775246/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)N(C)N=C1C(C)C)C(=O)[O-]) `REAL300004918900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918900 none CC#CCC(NC(=O)C1=C(Cl)N(C)N=C1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 5, 8, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 29, 41, 41, 75, 75, 75, 75, 75, 29, 6, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2] 77 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 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: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918900 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918900 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918900/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918900 Building REAL300004918901 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918901' /scratch/stefan/7775246/working/building/REAL300004918901 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918901 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918901/0 /scratch/stefan/7775246/working/building/REAL300004918901 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/907 `/scratch/stefan/7775246/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=C(C)C=C2)OC=N1)C(=O)[O-]) `REAL300004918901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918901 none CC#CCC(NC(=O)C1=C(C2=CC=C(C)C=C2)OC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 53, 13, 13, 1, 13, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 1, 53, 75, 75, 142, 142, 142, 142, 142, 53, 13, 6, 6, 6, 6, 6, 6, 6, 1] 175 rigid atoms, others: [37, 6, 8, 9, 10, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 636 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918901 none CC#CCC(NC(=O)C1=C(C2=CC=C(C)C=C2)OC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 96, 40, 40, 6, 40, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 96, 126, 126, 175, 175, 175, 175, 175, 96, 40, 1, 1, 2, 2, 2, 1, 1, 6] 175 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 829 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918901 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918901 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918901/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918901 Building REAL300004918902 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918902' /scratch/stefan/7775246/working/building/REAL300004918902 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918902 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918902/0 /scratch/stefan/7775246/working/building/REAL300004918902 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/908 `/scratch/stefan/7775246/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC2=CC=CC=C2N1)C(=O)[O-]) `REAL300004918902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918902 none CC#CCC(NC(=O)CNC(=O)C1=CC2=CC=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 85, 85, 25, 85, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 166, 166, 201, 201, 201, 201, 201, 135, 85, 25, 25, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 952 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918902 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918902 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918902/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918902 Building REAL300004918903 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918903' /scratch/stefan/7775246/working/building/REAL300004918903 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918903 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918903/0 /scratch/stefan/7775246/working/building/REAL300004918903 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/909 `/scratch/stefan/7775246/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C(COCCOC)=C1)C(=O)[O-]) `REAL300004918903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918903 none CC#CCC(NC(=O)C1=CC=C(F)C(COCCOC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 5, 12, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 21, 33, 37, 43, 1, 13, 20, 20, 32, 32, 32, 32, 32, 13, 5, 1, 1, 7, 7, 33, 33, 37, 37, 43, 43, 43, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918903 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918903 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918903/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918903 Building REAL300004918904 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918904' /scratch/stefan/7775246/working/building/REAL300004918904 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918904 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918904/0 /scratch/stefan/7775246/working/building/REAL300004918904 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/910 `/scratch/stefan/7775246/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)N(C)N=C2C(C)C)C(=O)[O-]) `REAL300004918904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918904 none CC#CCC(NC(=O)C1=CC2=C(S1)N(C)N=C2C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 46, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 46, 69, 69, 120, 120, 120, 120, 120, 46, 13, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 149 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 574 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918904 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918904 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918904/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918904 Building REAL300004918905 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918905' /scratch/stefan/7775246/working/building/REAL300004918905 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918905 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918905/0 /scratch/stefan/7775246/working/building/REAL300004918905 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/911 `/scratch/stefan/7775246/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(NS(=O)(=O)C2=C(C)ON=C2C)CCCC1)C(=O)[O-]) `REAL300004918905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918905 none CC#CCC(NC(=O)C1(NS(=O)(=O)C2=C(C)ON=C2C)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 5, 12, 8, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [6, 8, 9, 41, 43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918905 none CC#CCC(NC(=O)C1(NS(=O)(=O)C2=C(C)ON=C2C)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 5, 12, 8, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [10, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918905 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918905 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918905/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918905 Building REAL300004918906 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918906' /scratch/stefan/7775246/working/building/REAL300004918906 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918906 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918906/0 /scratch/stefan/7775246/working/building/REAL300004918906 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/912 `/scratch/stefan/7775246/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC(=O)C1=CC2=C(S1)N(C)N=C2C)C(=O)[O-]) `REAL300004918906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918906 none CC#CCC(NC(=O)C(C)NC(=O)C1=CC2=C(S1)N(C)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 133, 73, 73, 13, 73, 7, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 165, 165, 201, 201, 201, 201, 201, 133, 73, 13, 13, 13, 13, 7, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [38, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 988 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918906 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918906 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918906/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918906 Building REAL300004918907 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918907' /scratch/stefan/7775246/working/building/REAL300004918907 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918907 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918907/0 /scratch/stefan/7775246/working/building/REAL300004918907 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/913 `/scratch/stefan/7775246/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=C(C)N(C)N=C1C)C(=O)[O-]) `REAL300004918907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918907 none CC#CCC(NC(=O)C(C)NS(=O)(=O)C1=C(C)N(C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 5, 8, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 94, 94, 34, 94, 15, 34, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 153, 193, 193, 201, 201, 201, 201, 201, 153, 94, 34, 34, 34, 34, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 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: 1067 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918907 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918907 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918907/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918907 Building REAL300004918908 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918908' /scratch/stefan/7775246/working/building/REAL300004918908 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918908 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918908/0 /scratch/stefan/7775246/working/building/REAL300004918908 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/914 `/scratch/stefan/7775246/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C(C)(C)C)N=C1C1=CC=C(F)C=C1F)C(=O)[O-]) `REAL300004918908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918908 none CC#CCC(NC(=O)C1=CN(C(C)(C)C)N=C1C1=CC=C(F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 28, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 1, 7, 9, 9, 9, 28, 44, 44, 64, 64, 64, 64, 64, 28, 12, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918908 none CC#CCC(NC(=O)C1=CN(C(C)(C)C)N=C1C1=CC=C(F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 89, 46, 46, 9, 46, 9, 9, 9, 9, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 129, 129, 163, 163, 163, 163, 163, 89, 46, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918908 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918908 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918908/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918908 Building REAL300004918909 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918909' /scratch/stefan/7775246/working/building/REAL300004918909 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918909 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918909/0 /scratch/stefan/7775246/working/building/REAL300004918909 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/915 `/scratch/stefan/7775246/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C(C)=C1)C(=O)[O-]) `REAL300004918909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918909 none CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 26, 40, 40, 78, 78, 78, 78, 78, 26, 7, 1, 1, 9, 9, 2, 2, 2, 1] 148 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918909 none CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 70, 32, 32, 7, 32, 2, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 70, 92, 92, 148, 148, 148, 148, 148, 70, 32, 9, 9, 1, 1, 9, 9, 9, 9] 148 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918909 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918909 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918909/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918909 Building REAL300004918910 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918910' /scratch/stefan/7775246/working/building/REAL300004918910 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918910 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918910/0 /scratch/stefan/7775246/working/building/REAL300004918910 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/916 `/scratch/stefan/7775246/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C=C1C)C(=O)[O-]) `REAL300004918910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918910 none CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 33, 44, 44, 71, 71, 71, 71, 71, 33, 10, 1, 1, 6, 6, 1, 2, 2, 2] 140 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918910 none CC#CCC(NC(=O)C1=CC=C(N2C=NC=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 78, 37, 37, 6, 37, 2, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 78, 96, 96, 140, 140, 140, 140, 140, 78, 37, 6, 6, 1, 1, 6, 7, 7, 7] 140 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 632 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918910 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918910 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918910/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918910 Building REAL300004918911 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918911' /scratch/stefan/7775246/working/building/REAL300004918911 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918911 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918911/0 /scratch/stefan/7775246/working/building/REAL300004918911 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/917 `/scratch/stefan/7775246/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=C3OCCOC3=C2)OC=N1)C(=O)[O-]) `REAL300004918911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918911 none CC#CCC(NC(=O)C1=C(C2=CC=C3OCCOC3=C2)OC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 12, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 32, 12, 12, 1, 12, 1, 1, 1, 11, 11, 10, 11, 11, 11, 11, 11, 11, 1, 1, 1, 32, 54, 54, 88, 88, 88, 88, 88, 32, 12, 11, 11, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [6, 8, 9, 10, 40, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918911 none CC#CCC(NC(=O)C1=C(C2=CC=C3OCCOC3=C2)OC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 12, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 55, 55, 11, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 124, 151, 151, 201, 201, 201, 201, 201, 124, 55, 1, 1, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40]) total number of confs: 940 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918911 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918911 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918911/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918911 Building REAL300004918912 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918912' /scratch/stefan/7775246/working/building/REAL300004918912 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918912 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918912/0 /scratch/stefan/7775246/working/building/REAL300004918912 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/918 `/scratch/stefan/7775246/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N1C)C(=O)[O-]) `REAL300004918912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918912 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1, 40, 65, 65, 95, 95, 95, 95, 95, 40, 12, 1, 1, 4, 4, 4, 4, 4, 2, 2, 2] 115 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 494 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918912 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 74, 30, 30, 4, 30, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 74, 93, 93, 116, 116, 116, 116, 116, 74, 30, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4] 116 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 547 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918912 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918912 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918912/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918912 Building REAL300004918913 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918913' /scratch/stefan/7775246/working/building/REAL300004918913 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918913 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918913/0 /scratch/stefan/7775246/working/building/REAL300004918913 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/919 `/scratch/stefan/7775246/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CS2)N=N1)C(=O)[O-]) `REAL300004918913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918913 none CC#CCC(NC(=O)C1=CN(CC2=CC=CS2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 14, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 16, 6, 6, 1, 6, 1, 1, 1, 1, 9, 21, 21, 21, 21, 1, 1, 16, 23, 23, 33, 33, 33, 33, 33, 16, 6, 1, 9, 9, 21, 21, 21] 201 rigid atoms, others: [6, 8, 9, 10, 11, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918913 none CC#CCC(NC(=O)C1=CN(CC2=CC=CS2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 14, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 59, 59, 21, 59, 21, 21, 4, 1, 1, 1, 1, 1, 1, 21, 21, 102, 147, 147, 201, 201, 201, 201, 201, 102, 59, 21, 4, 4, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 993 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918913 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918913 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918913/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918913 Building REAL300004918914 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918914' /scratch/stefan/7775246/working/building/REAL300004918914 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918914 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918914/0 /scratch/stefan/7775246/working/building/REAL300004918914 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/920 `/scratch/stefan/7775246/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=C(C)N(C)N=C1C)C(=O)[O-]) `REAL300004918914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918914 none CC#CCC(NC(=O)C(C)CC1=C(C)N(C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 8, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 56, 56, 13, 56, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 135, 135, 201, 201, 201, 201, 201, 110, 56, 13, 13, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 956 number of broken/clashed sets: 170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918914 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918914 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918914/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918914 Building REAL300004918915 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918915' /scratch/stefan/7775246/working/building/REAL300004918915 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918915 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918915/0 /scratch/stefan/7775246/working/building/REAL300004918915 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/921 `/scratch/stefan/7775246/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC(C2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004918915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918915 none CC#CCC(NC(=O)C1CCC(C2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 22, 39, 39, 77, 77, 77, 77, 77, 22, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1] 112 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 44, 43, 18, 19, 41, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918915 none CC#CCC(NC(=O)C1CCC(C2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 48, 16, 16, 4, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 48, 73, 73, 112, 112, 112, 112, 112, 48, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4] 112 rigid atoms, others: [36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918915 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918915 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918915/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918915 Building REAL300004918916 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918916' /scratch/stefan/7775246/working/building/REAL300004918916 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918916 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918916/0 /scratch/stefan/7775246/working/building/REAL300004918916 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/922 `/scratch/stefan/7775246/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C([N+](=O)[O-])C(OC)=C1)C(=O)[O-]) `REAL300004918916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918916 none CC#CCC(NC(=O)COC1=CC=C([N+](=O)[O-])C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 149, 85, 85, 20, 85, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 149, 172, 172, 187, 187, 187, 187, 187, 149, 85, 20, 20, 1, 1, 4, 4, 4, 1] 201 rigid atoms, others: [33, 34, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 857 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918916 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918916 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918916/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918916 Building REAL300004918917 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918917' /scratch/stefan/7775246/working/building/REAL300004918917 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918917 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918917/0 /scratch/stefan/7775246/working/building/REAL300004918917 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/923 `/scratch/stefan/7775246/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCSCC2)=CN1)C(=O)[O-]) `REAL300004918917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918917 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCSCC2)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 14, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 16, 5, 5, 1, 5, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 29, 29, 1, 1, 16, 25, 25, 34, 34, 34, 34, 34, 16, 6, 1, 29, 29, 30, 30, 30, 30, 29, 29, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918917 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCSCC2)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 14, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 82, 82, 30, 82, 30, 30, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 30, 30, 138, 168, 168, 201, 201, 201, 201, 201, 138, 82, 30, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918917 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918917 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918917/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918917 Building REAL300004918918 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918918' /scratch/stefan/7775246/working/building/REAL300004918918 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918918 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918918/0 /scratch/stefan/7775246/working/building/REAL300004918918 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/924 `/scratch/stefan/7775246/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(F)C=C1F)C(=O)[O-]) `REAL300004918918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918918 none CC#CCC(NC(=O)CCCOC1=CC=C(F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 103, 103, 52, 103, 50, 32, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 160, 160, 201, 201, 201, 201, 201, 136, 103, 52, 52, 50, 50, 32, 32, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1017 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918918 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918918 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918918/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918918 Building REAL300004918919 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918919' /scratch/stefan/7775246/working/building/REAL300004918919 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918919 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918919/0 /scratch/stefan/7775246/working/building/REAL300004918919 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/925 `/scratch/stefan/7775246/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=NOC(C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004918919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918919 none CC#CCC(NC(=O)CNC(=O)C1=NOC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 145, 88, 88, 18, 88, 3, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 145, 150, 150, 194, 194, 194, 194, 194, 145, 88, 18, 18, 4, 6, 6, 1, 6, 6, 1] 201 rigid atoms, others: [41, 10, 12, 13, 14, 15, 16, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 846 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918919 none CC#CCC(NC(=O)CNC(=O)C1=NOC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 186, 148, 148, 52, 148, 13, 14, 6, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 186, 189, 189, 201, 201, 201, 201, 201, 186, 148, 52, 52, 14, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 767 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918919 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918919 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918919/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918919 Building REAL300004918920 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918920' /scratch/stefan/7775246/working/building/REAL300004918920 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918920 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918920/0 /scratch/stefan/7775246/working/building/REAL300004918920 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/926 `/scratch/stefan/7775246/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(S(C)(=O)=O)CCCC1)C(=O)[O-]) `REAL300004918920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918920 none CC#CCC(NC(=O)C1(S(C)(=O)=O)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 36, 9, 9, 1, 9, 1, 1, 7, 7, 7, 1, 1, 1, 1, 36, 53, 53, 82, 82, 82, 82, 82, 36, 9, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 112 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 408 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918920 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918920 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918920/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918920 Building REAL300004918921 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918921' /scratch/stefan/7775246/working/building/REAL300004918921 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918921 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918921/0 /scratch/stefan/7775246/working/building/REAL300004918921 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/927 `/scratch/stefan/7775246/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC(F)=C2)N=N1)C(=O)[O-]) `REAL300004918921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918921 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC(F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 30, 9, 9, 1, 9, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 30, 42, 42, 65, 65, 65, 65, 65, 30, 9, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918921 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC(F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 40, 40, 7, 40, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 120, 153, 153, 201, 201, 201, 201, 201, 120, 40, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918921 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918921 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918921/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918921 Building REAL300004918922 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918922' /scratch/stefan/7775246/working/building/REAL300004918922 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918922 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918922/0 /scratch/stefan/7775246/working/building/REAL300004918922 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/928 `/scratch/stefan/7775246/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC=C2F)N=N1)C(=O)[O-]) `REAL300004918922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918922 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC=C2F)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 31, 9, 9, 1, 9, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 31, 47, 47, 74, 74, 74, 74, 74, 31, 9, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918922 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC=C2F)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 44, 44, 7, 44, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 117, 151, 151, 201, 201, 201, 201, 201, 117, 44, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918922 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918922 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918922/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918922 Building REAL300004918923 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918923' /scratch/stefan/7775246/working/building/REAL300004918923 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918923 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918923/0 /scratch/stefan/7775246/working/building/REAL300004918923 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/929 `/scratch/stefan/7775246/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CNC2=CC=C([N+](=O)[O-])C=C12)C(=O)[O-]) `REAL300004918923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918923 none CC#CCC(NC(=O)C1=CNC2=CC=C([N+](=O)[O-])C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 48, 48, 80, 80, 80, 80, 80, 36, 11, 1, 1, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918923 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918923 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918923/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918923 Building REAL300004918924 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918924' /scratch/stefan/7775246/working/building/REAL300004918924 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918924 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918924/0 /scratch/stefan/7775246/working/building/REAL300004918924 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/930 `/scratch/stefan/7775246/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=NC=CC=N2)S1)C(=O)[O-]) `REAL300004918924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918924 none CC#CCC(NC(=O)C1=CN=C(C2=NC=CC=N2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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: [97, 97, 97, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 3, 7, 7, 1, 39, 59, 59, 97, 97, 97, 97, 97, 39, 13, 1, 7, 3, 7] 127 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918924 none CC#CCC(NC(=O)C1=CN=C(C2=NC=CC=N2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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, 87, 53, 53, 13, 53, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 87, 105, 105, 127, 127, 127, 127, 127, 87, 53, 13, 1, 1, 1] 127 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918924 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918924 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918924/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918924 Building REAL300004918925 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918925' /scratch/stefan/7775246/working/building/REAL300004918925 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918925 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918925/0 /scratch/stefan/7775246/working/building/REAL300004918925 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/931 `/scratch/stefan/7775246/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)C(C)CC)C1)C(=O)[O-]) `REAL300004918925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918925 none CC#CCC(NC(=O)C1CCCN(C(=O)C(C)CC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 15, 1, 25, 39, 39, 63, 63, 63, 63, 63, 25, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 16, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 46, 47, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 367 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918925 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918925 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918925/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918925 Building REAL300004918926 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918926' /scratch/stefan/7775246/working/building/REAL300004918926 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918926 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918926/0 /scratch/stefan/7775246/working/building/REAL300004918926 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/932 `/scratch/stefan/7775246/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1OC)C(=O)[O-]) `REAL300004918926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918926 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 46, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 46, 68, 68, 112, 112, 112, 112, 112, 46, 13, 1, 1, 1, 3, 3, 3] 135 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918926 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918926 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918926/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918926 Building REAL300004918927 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918927' /scratch/stefan/7775246/working/building/REAL300004918927 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918927 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918927/0 /scratch/stefan/7775246/working/building/REAL300004918927 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/933 `/scratch/stefan/7775246/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-]) `REAL300004918927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918927 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 34, 9, 9, 1, 9, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 34, 57, 57, 92, 92, 92, 92, 92, 34, 9, 4, 4, 4, 4] 111 rigid atoms, others: [6, 8, 9, 10, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918927 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 62, 18, 18, 4, 18, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 62, 79, 79, 111, 111, 111, 111, 111, 62, 18, 1, 1, 1, 1] 111 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918927 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918927 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918927/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918927 Building REAL300004918928 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918928' /scratch/stefan/7775246/working/building/REAL300004918928 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918928 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918928/0 /scratch/stefan/7775246/working/building/REAL300004918928 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/934 `/scratch/stefan/7775246/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(Br)C=C1C)C(=O)[O-]) `REAL300004918928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918928 none CC#CCC(NC(=O)CSC1=CC=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 86, 86, 26, 86, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 151, 151, 201, 201, 201, 201, 201, 122, 86, 26, 26, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 979 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918928 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918928 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918928/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918928 Building REAL300004918929 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918929' /scratch/stefan/7775246/working/building/REAL300004918929 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918929 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918929/0 /scratch/stefan/7775246/working/building/REAL300004918929 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/935 `/scratch/stefan/7775246/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918929 none CC#CCC(NC(=O)C1=CC=C(OC)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 1, 1, 2, 2, 1, 30, 50, 50, 106, 106, 106, 106, 106, 30, 7, 1, 1, 4, 4, 4, 1] 138 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 14, 15, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918929 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918929 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918929/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918929 Building REAL300004918930 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918930' /scratch/stefan/7775246/working/building/REAL300004918930 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918930 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918930/0 /scratch/stefan/7775246/working/building/REAL300004918930 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/936 `/scratch/stefan/7775246/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918930 none CC#CCC(NC(=O)CC(C1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 94, 43, 43, 9, 43, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 94, 129, 129, 189, 189, 189, 189, 189, 94, 43, 9, 9, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 929 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918930 none CC#CCC(NC(=O)CC(C1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 89, 44, 44, 9, 44, 3, 1, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 89, 127, 127, 183, 183, 183, 183, 183, 89, 44, 9, 9, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 9, 42, 43, 44, 16, 17, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 907 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918930 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918930 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918930/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918930 Building REAL300004918931 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918931' /scratch/stefan/7775246/working/building/REAL300004918931 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918931 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918931/0 /scratch/stefan/7775246/working/building/REAL300004918931 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/937 `/scratch/stefan/7775246/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004918931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918931 none CC#CCC(NC(=O)C1=CC=CC=C1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 10, 16, 16, 29, 47, 47, 81, 81, 81, 81, 81, 29, 9, 1, 1, 1, 1, 10, 10, 16, 16, 10, 16, 16] 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, 40, 41]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918931 none CC#CCC(NC(=O)C1=CC=CC=C1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 55, 55, 16, 55, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 118, 151, 151, 201, 201, 201, 201, 201, 118, 55, 16, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918931 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918931 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918931/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918931 Building REAL300004918932 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918932' /scratch/stefan/7775246/working/building/REAL300004918932 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918932 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918932/0 /scratch/stefan/7775246/working/building/REAL300004918932 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/938 `/scratch/stefan/7775246/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(OC)C=C1OC)C(=O)[O-]) `REAL300004918932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918932 none CC#CCC(NC(=O)C1=CC(OC)=C(OC)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 30, 12, 12, 1, 12, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 4, 30, 53, 53, 87, 87, 87, 87, 87, 30, 12, 1, 4, 4, 4, 3, 3, 3, 1, 4, 4, 4] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 13, 14, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918932 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918932 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918932/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918932 Building REAL300004918933 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918933' /scratch/stefan/7775246/working/building/REAL300004918933 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918933 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918933/0 /scratch/stefan/7775246/working/building/REAL300004918933 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/939 `/scratch/stefan/7775246/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918933 none CC#CCC(NC(=O)C=CC1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 115, 44, 44, 5, 45, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 115, 142, 142, 198, 198, 198, 198, 198, 115, 45, 5, 5, 1, 1, 1, 1] 198 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 895 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918933 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918933 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918933/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918933 Building REAL300004918934 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918934' /scratch/stefan/7775246/working/building/REAL300004918934 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918934 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918934/0 /scratch/stefan/7775246/working/building/REAL300004918934 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/940 `/scratch/stefan/7775246/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC=CC=C2S1)C(=O)[O-]) `REAL300004918934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918934 none CC#CCC(NC(=O)C1=C(Cl)C2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 36, 36, 60, 60, 60, 60, 60, 27, 7, 1, 1, 1, 1] 60 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918934 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918934 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918934/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918934 Building REAL300004918935 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918935' /scratch/stefan/7775246/working/building/REAL300004918935 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918935 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918935/0 /scratch/stefan/7775246/working/building/REAL300004918935 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/941 `/scratch/stefan/7775246/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N2CCCCC2)=C1)C(=O)[O-]) `REAL300004918935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918935 none CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 29, 41, 41, 71, 71, 71, 71, 71, 29, 7, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 198 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 49, 23] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 343 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918935 none CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 84, 21, 21, 5, 21, 5, 5, 5, 5, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 84, 116, 116, 198, 198, 198, 198, 198, 84, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 198 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 48, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49]) total number of confs: 946 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918935 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918935 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918935/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918935 Building REAL300004918936 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918936' /scratch/stefan/7775246/working/building/REAL300004918936 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918936 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918936/0 /scratch/stefan/7775246/working/building/REAL300004918936 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/942 `/scratch/stefan/7775246/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCOCC2)=CC=C1C)C(=O)[O-]) `REAL300004918936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918936 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCOCC2)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 16, 9, 9, 1, 9, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 19, 19, 1, 1, 1, 1, 16, 30, 30, 43, 43, 43, 43, 43, 16, 9, 1, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 43, 6, 8, 9, 10, 11, 44, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918936 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCOCC2)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 133, 89, 89, 19, 89, 19, 19, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 19, 19, 18, 18, 133, 166, 166, 201, 201, 201, 201, 201, 133, 89, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47]) total number of confs: 957 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918936 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918936 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918936/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918936 Building REAL300004918937 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918937' /scratch/stefan/7775246/working/building/REAL300004918937 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918937 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918937/0 /scratch/stefan/7775246/working/building/REAL300004918937 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/943 `/scratch/stefan/7775246/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N2CCOCC2)=C1)C(=O)[O-]) `REAL300004918937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918937 none CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N2CCOCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 1, 29, 41, 41, 72, 72, 72, 72, 72, 29, 7, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 47, 23] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918937 none CC#CCC(NC(=O)C1=CC=C(C)C(S(=O)(=O)N2CCOCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 84, 21, 21, 5, 21, 5, 5, 5, 5, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 84, 117, 117, 201, 201, 201, 201, 201, 84, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47]) total number of confs: 959 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918937 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918937 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918937/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918937 Building REAL300004918938 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918938' /scratch/stefan/7775246/working/building/REAL300004918938 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918938 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918938/0 /scratch/stefan/7775246/working/building/REAL300004918938 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/944 `/scratch/stefan/7775246/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC(C)=C1C)C(=O)[O-]) `REAL300004918938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918938 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC(C)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 31, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 9, 17, 17, 17, 17, 31, 51, 51, 84, 84, 84, 84, 84, 31, 12, 1, 1, 1, 1, 6, 17, 17, 9, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 466 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918938 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC(C)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 72, 72, 17, 72, 17, 17, 17, 17, 17, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 160, 160, 201, 201, 201, 201, 201, 130, 72, 17, 17, 17, 17, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46]) total number of confs: 941 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918938 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918938 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918938/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918938 Building REAL300004918939 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918939' /scratch/stefan/7775246/working/building/REAL300004918939 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918939 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918939/0 /scratch/stefan/7775246/working/building/REAL300004918939 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/945 `/scratch/stefan/7775246/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC=C(F)C=C2S1)C(=O)[O-]) `REAL300004918939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918939 none CC#CCC(NC(=O)C1=C(Cl)C2=CC=C(F)C=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 36, 36, 62, 62, 62, 62, 62, 27, 7, 1, 1, 1] 62 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918939 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918939 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918939/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918939 Building REAL300004918940 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918940' /scratch/stefan/7775246/working/building/REAL300004918940 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918940 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918940/0 /scratch/stefan/7775246/working/building/REAL300004918940 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/946 `/scratch/stefan/7775246/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)ON=C1C1=C(F)C=CC=C1Cl)C(=O)[O-]) `REAL300004918940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918940 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=C(F)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 40, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 7, 7, 7, 40, 65, 65, 100, 100, 100, 100, 100, 40, 13, 1, 1, 1, 7, 2, 7] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918940 none CC#CCC(NC(=O)C1=C(C)ON=C1C1=C(F)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 8, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 123, 55, 55, 7, 55, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 157, 157, 201, 201, 201, 201, 201, 123, 55, 7, 7, 7, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 939 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918940 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918940 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918940/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918940 Building REAL300004918941 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918941' /scratch/stefan/7775246/working/building/REAL300004918941 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918941 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918941/0 /scratch/stefan/7775246/working/building/REAL300004918941 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/947 `/scratch/stefan/7775246/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004918941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918941 none CC#CCC(NC(=O)CC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 47, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 1, 47, 79, 79, 152, 152, 152, 152, 152, 47, 11, 3, 3, 1, 1, 1, 1] 152 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918941 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918941 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918941/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918941 Building REAL300004918942 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918942' /scratch/stefan/7775246/working/building/REAL300004918942 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918942 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918942/0 /scratch/stefan/7775246/working/building/REAL300004918942 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/948 `/scratch/stefan/7775246/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CC3CC(CC(Br)(C3)C1)C2)C(=O)[O-]) `REAL300004918942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918942 none CC#CCC(NC(=O)C12CC3CC(CC(Br)(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'Br', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 17, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 42, 42, 83, 83, 83, 83, 83, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918942 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918942 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918942/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918942 Building REAL300004918943 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918943' /scratch/stefan/7775246/working/building/REAL300004918943 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918943 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918943/0 /scratch/stefan/7775246/working/building/REAL300004918943 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/949 `/scratch/stefan/7775246/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCCC2)=CC=C1C)C(=O)[O-]) `REAL300004918943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918943 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCCC2)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 17, 9, 9, 1, 9, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 20, 1, 1, 1, 1, 17, 31, 31, 43, 43, 43, 43, 43, 17, 9, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 45, 46, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918943 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCCC2)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 133, 89, 89, 20, 89, 20, 20, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 133, 167, 167, 201, 201, 201, 201, 201, 133, 89, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 21, 21, 21] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 44, 14, 15, 16, 17, 18, 19, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 946 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918943 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918943 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918943/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918943 Building REAL300004918944 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918944' /scratch/stefan/7775246/working/building/REAL300004918944 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918944 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918944/0 /scratch/stefan/7775246/working/building/REAL300004918944 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/950 `/scratch/stefan/7775246/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)N(C1=CC=C(F)C=C1)N=C2C)C(=O)[O-]) `REAL300004918944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918944 none CC#CCC(NC(=O)C1=CC2=C(S1)N(C1=CC=C(F)C=C1)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 50, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 1, 50, 76, 76, 129, 129, 129, 129, 129, 50, 13, 1, 6, 6, 6, 6, 2, 2, 2] 133 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918944 none CC#CCC(NC(=O)C1=CC2=C(S1)N(C1=CC=C(F)C=C1)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 93, 39, 39, 6, 39, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 93, 112, 112, 133, 133, 133, 133, 133, 93, 39, 6, 1, 1, 1, 1, 6, 6, 6] 133 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918944 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918944 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918944/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918944 Building REAL300004918945 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918945' /scratch/stefan/7775246/working/building/REAL300004918945 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918945 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918945/0 /scratch/stefan/7775246/working/building/REAL300004918945 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/951 `/scratch/stefan/7775246/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(C)S1)C(=O)[O-]) `REAL300004918945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918945 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 134, 85, 85, 22, 85, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 134, 163, 163, 201, 201, 201, 201, 201, 134, 84, 21, 21, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 946 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918945 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918945 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918945/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918945 Building REAL300004918946 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918946' /scratch/stefan/7775246/working/building/REAL300004918946 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918946 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918946/0 /scratch/stefan/7775246/working/building/REAL300004918946 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/952 `/scratch/stefan/7775246/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(C(C)(C)C)C=C2)C=C1)C(=O)[O-]) `REAL300004918946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918946 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(C(C)(C)C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 9, 9, 9, 9, 17, 17, 17, 9, 9, 1, 1, 7, 8, 8, 18, 18, 18, 18, 18, 7, 3, 1, 1, 8, 8, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 1, 1] 55 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 53, 54, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918946 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=C(C(C)(C)C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 54, 54, 38, 17, 17, 2, 17, 2, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 38, 39, 39, 54, 54, 54, 54, 54, 38, 17, 9, 9, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 9, 9] 55 rigid atoms, others: [40, 41, 13, 14, 15, 16, 17, 18, 51, 52, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918946 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918946 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918946/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918946 Building REAL300004918947 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918947' /scratch/stefan/7775246/working/building/REAL300004918947 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918947 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918947/0 /scratch/stefan/7775246/working/building/REAL300004918947 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/953 `/scratch/stefan/7775246/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CSC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-]) `REAL300004918947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918947 none CC#CCC(NC(=O)C1=CC=C(CSC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 23, 44, 44, 23, 23, 44, 44, 1, 1, 7, 12, 12, 24, 24, 24, 24, 24, 7, 3, 1, 1, 6, 6, 44, 44, 44, 44, 1, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918947 none CC#CCC(NC(=O)C1=CC=C(CSC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 70, 70, 34, 70, 21, 44, 44, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 125, 156, 156, 201, 201, 201, 201, 201, 125, 70, 44, 44, 21, 21, 1, 1, 1, 1, 44, 44] 201 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 1065 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918947 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918947 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918947/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918947 Building REAL300004918948 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918948' /scratch/stefan/7775246/working/building/REAL300004918948 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918948 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918948/0 /scratch/stefan/7775246/working/building/REAL300004918948 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/954 `/scratch/stefan/7775246/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC2=C(C=C1)N(CC)C1=C2C=CC=C1)C(=O)[O-]) `REAL300004918948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918948 none CC#CCC(NC(=O)C=CC1=CC2=C(C=C1)N(CC)C1=C2C=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 70, 31, 31, 5, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 70, 101, 101, 152, 152, 152, 152, 152, 70, 31, 5, 5, 1, 1, 1, 2, 2, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 37, 38, 39, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 753 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918948 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918948 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918948/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918948 Building REAL300004918949 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918949' /scratch/stefan/7775246/working/building/REAL300004918949 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918949 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918949/0 /scratch/stefan/7775246/working/building/REAL300004918949 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/955 `/scratch/stefan/7775246/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1CCS(=O)(=O)C1)C(=O)[O-]) `REAL300004918949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918949 none CC#CCC(NC(=O)CSC1CCS(=O)(=O)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 14, 11, 11, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 73, 73, 24, 73, 7, 1, 1, 1, 1, 1, 1, 1, 1, 124, 161, 161, 201, 201, 201, 201, 201, 123, 73, 24, 24, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 988 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918949 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918949 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918949/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918949 Building REAL300004918950 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918950' /scratch/stefan/7775246/working/building/REAL300004918950 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918950 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918950/0 /scratch/stefan/7775246/working/building/REAL300004918950 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/956 `/scratch/stefan/7775246/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC)C=C1)C(=O)[O-]) `REAL300004918950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918950 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 1, 1, 15, 25, 25, 55, 55, 55, 55, 55, 15, 4, 1, 1, 13, 13, 13, 13, 1, 1] 130 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918950 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918950 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918950/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918950 Building REAL300004918951 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918951' /scratch/stefan/7775246/working/building/REAL300004918951 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918951 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918951/0 /scratch/stefan/7775246/working/building/REAL300004918951 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/957 `/scratch/stefan/7775246/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC)C(=O)[O-]) `REAL300004918951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918951 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 45, 66, 66, 118, 118, 118, 118, 118, 45, 12, 1, 1, 1, 4, 4, 4] 142 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918951 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918951 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918951/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918951 Building REAL300004918952 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918952' /scratch/stefan/7775246/working/building/REAL300004918952 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918952 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918952/0 /scratch/stefan/7775246/working/building/REAL300004918952 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/958 `/scratch/stefan/7775246/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OCC)=C(OC)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918952 none CC#CCC(NC(=O)C1=CC(OCC)=C(OC)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 5, 1, 12, 5, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 13, 5, 5, 1, 5, 1, 1, 1, 1, 9, 33, 1, 1, 3, 1, 1, 1, 2, 2, 13, 23, 23, 48, 48, 48, 48, 48, 13, 5, 1, 33, 33, 34, 34, 34, 4, 4, 4, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 14, 15, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918952 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918952 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918952/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918952 Building REAL300004918953 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918953' /scratch/stefan/7775246/working/building/REAL300004918953 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918953 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918953/0 /scratch/stefan/7775246/working/building/REAL300004918953 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/959 `/scratch/stefan/7775246/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(CC(C)C)C=C1)C(=O)[O-]) `REAL300004918953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918953 none CC#CCC(NC(=O)CC1=CC=C(CC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 32, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 32, 48, 48, 88, 88, 88, 88, 88, 32, 9, 3, 3, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 17, 18, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 452 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918953 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918953 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918953/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918953 Building REAL300004918954 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918954' /scratch/stefan/7775246/working/building/REAL300004918954 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918954 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918954/0 /scratch/stefan/7775246/working/building/REAL300004918954 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/960 `/scratch/stefan/7775246/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004918954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918954 none CC#CCC(NC(=O)CCCNC1=CC=C([N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 190, 136, 136, 42, 136, 24, 10, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 190, 190, 190, 201, 201, 201, 201, 201, 190, 136, 42, 42, 24, 24, 10, 10, 4, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 831 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918954 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918954 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918954/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918954 Building REAL300004918955 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918955' /scratch/stefan/7775246/working/building/REAL300004918955 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918955 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918955/0 /scratch/stefan/7775246/working/building/REAL300004918955 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/961 `/scratch/stefan/7775246/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004918955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918955 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 68, 27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 68, 108, 108, 158, 158, 158, 158, 158, 68, 27, 6, 6, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 830 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918955 none CC#CCC(NC(=O)CC1=C(C)N(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 50, 50, 12, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 110, 151, 151, 201, 201, 201, 201, 201, 110, 50, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44]) total number of confs: 1012 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918955 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918955 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918955/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918955 Building REAL300004918956 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918956' /scratch/stefan/7775246/working/building/REAL300004918956 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918956 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918956/0 /scratch/stefan/7775246/working/building/REAL300004918956 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/962 `/scratch/stefan/7775246/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=C(OC(F)F)C=C1)C(=O)[O-]) `REAL300004918956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918956 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=C(OC(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 20, 40, 40, 3, 3, 18, 27, 27, 43, 43, 43, 43, 43, 18, 9, 1, 1, 1, 1, 3, 3, 3, 40, 3, 3] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918956 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=C(OC(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 25, 14, 14, 3, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 12, 27, 27, 1, 1, 25, 35, 35, 54, 54, 54, 54, 54, 25, 14, 3, 3, 3, 3, 3, 1, 1, 27, 1, 1] 201 rigid atoms, others: [40, 41, 43, 44, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918956 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918956 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918956/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918956 Building REAL300004918957 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918957' /scratch/stefan/7775246/working/building/REAL300004918957 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918957 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918957/0 /scratch/stefan/7775246/working/building/REAL300004918957 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/963 `/scratch/stefan/7775246/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2N=CC=C2C)C=C1)C(=O)[O-]) `REAL300004918957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918957 none CC#CCC(NC(=O)C1=CC=C(N2N=CC=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 15, 23, 23, 43, 43, 43, 43, 43, 15, 4, 1, 1, 10, 10, 10, 10, 10, 1, 1] 118 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 204 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918957 none CC#CCC(NC(=O)C1=CC=C(N2N=CC=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 58, 20, 20, 10, 20, 9, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 58, 75, 75, 118, 118, 118, 118, 118, 58, 20, 10, 10, 1, 1, 2, 2, 2, 10, 10] 118 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 542 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918957 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918957 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918957/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918957 Building REAL300004918958 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918958' /scratch/stefan/7775246/working/building/REAL300004918958 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918958 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918958/0 /scratch/stefan/7775246/working/building/REAL300004918958 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/964 `/scratch/stefan/7775246/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(N2CCCC2=O)=C1)C(=O)[O-]) `REAL300004918958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918958 none CC#CCC(NC(=O)C1=CC=CC(N2CCCC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 23, 40, 40, 76, 76, 76, 76, 76, 23, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918958 none CC#CCC(NC(=O)C1=CC=CC(N2CCCC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 85, 30, 30, 9, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 85, 116, 116, 201, 201, 201, 201, 201, 85, 30, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39]) total number of confs: 918 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918958 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918958 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918958/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918958 Building REAL300004918959 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918959' /scratch/stefan/7775246/working/building/REAL300004918959 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918959 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918959/0 /scratch/stefan/7775246/working/building/REAL300004918959 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/965 `/scratch/stefan/7775246/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC=CN=C1C1=NC2=CC=CC=C2S1)C(=O)[O-]) `REAL300004918959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918959 none CC#CCC(NC(=O)C1=NC=CN=C1C1=NC2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 32, 54, 54, 87, 87, 87, 87, 87, 32, 10, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918959 none CC#CCC(NC(=O)C1=NC=CN=C1C1=NC2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 56, 56, 11, 56, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 152, 152, 201, 201, 201, 201, 201, 117, 56, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918959 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918959 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918959/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918959 Building REAL300004918960 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918960' /scratch/stefan/7775246/working/building/REAL300004918960 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918960 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918960/0 /scratch/stefan/7775246/working/building/REAL300004918960 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/966 `/scratch/stefan/7775246/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)OC)C=C1)C(=O)[O-]) `REAL300004918960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918960 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N(C)OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 39, 1, 1, 8, 12, 12, 26, 26, 26, 26, 26, 8, 3, 1, 1, 25, 25, 25, 39, 39, 39, 1, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 40, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918960 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918960 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918960/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918960 Building REAL300004918961 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918961' /scratch/stefan/7775246/working/building/REAL300004918961 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918961 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918961/0 /scratch/stefan/7775246/working/building/REAL300004918961 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/967 `/scratch/stefan/7775246/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)N(CC)CC)C=C1)C(=O)[O-]) `REAL300004918961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918961 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)N(CC)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 5, 3, 3, 2, 3, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 10, 21, 1, 1, 5, 7, 7, 22, 22, 22, 22, 22, 5, 3, 2, 2, 2, 2, 1, 1, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 1, 1] 69 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 50, 51, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918961 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918961 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918961/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918961 Building REAL300004918962 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918962' /scratch/stefan/7775246/working/building/REAL300004918962 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918962 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918962/0 /scratch/stefan/7775246/working/building/REAL300004918962 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/968 `/scratch/stefan/7775246/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC1=CC=C(C(F)(F)F)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918962 none CC#CCC(NC(=O)CCNC1=CC=C(C(F)(F)F)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 172, 98, 98, 23, 98, 19, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 176, 189, 189, 199, 199, 199, 199, 198, 176, 98, 23, 23, 19, 19, 4, 1, 1, 1] 199 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 863 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918962 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918962 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918962/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918962 Building REAL300004918963 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918963' /scratch/stefan/7775246/working/building/REAL300004918963 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918963 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918963/0 /scratch/stefan/7775246/working/building/REAL300004918963 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/969 `/scratch/stefan/7775246/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(OCC)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004918963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918963 none CC#CCC(NC(=O)C1=CC(OC)=C(OCC)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 12, 5, 5, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 13, 5, 5, 1, 5, 1, 1, 1, 1, 4, 1, 1, 9, 31, 1, 1, 1, 2, 2, 13, 23, 23, 45, 45, 45, 45, 45, 13, 5, 1, 4, 4, 4, 31, 31, 32, 32, 32, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 13, 14, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918963 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918963 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918963/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918963 Building REAL300004918964 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918964' /scratch/stefan/7775246/working/building/REAL300004918964 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918964 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918964/0 /scratch/stefan/7775246/working/building/REAL300004918964 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/970 `/scratch/stefan/7775246/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004918964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918964 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 46, 46, 18, 46, 46, 11, 27, 42, 42, 72, 72, 72, 72, 72, 27, 10, 1, 1, 1, 1, 11, 46, 46, 46, 46, 46] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918964 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 108, 108, 46, 108, 46, 46, 46, 46, 46, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 145, 174, 174, 201, 201, 201, 201, 201, 145, 108, 46, 46, 46, 46, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 861 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918964 none CC#CCC(NC(=O)C1=CC=CC=C1C1=NC=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 81, 47, 47, 11, 47, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 81, 113, 113, 172, 172, 172, 172, 172, 81, 47, 11, 11, 11, 11, 1, 7, 7, 6, 7, 7] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918964 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918964 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918964/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918964 Building REAL300004918965 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918965' /scratch/stefan/7775246/working/building/REAL300004918965 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918965 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918965/0 /scratch/stefan/7775246/working/building/REAL300004918965 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/971 `/scratch/stefan/7775246/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CSC=N1)C(=O)[O-]) `REAL300004918965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918965 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CSC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 24, 36, 36, 36, 36, 29, 45, 45, 80, 80, 80, 80, 80, 29, 12, 1, 1, 1, 1, 24, 24, 36, 36] 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]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918965 none CC#CCC(NC(=O)C1=CC=CC=C1OCC1=CSC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 82, 82, 36, 82, 36, 36, 36, 36, 36, 22, 5, 1, 1, 1, 1, 1, 1, 121, 151, 151, 201, 201, 201, 201, 201, 121, 82, 36, 36, 36, 36, 5, 5, 1, 1] 201 rigid atoms, others: [37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 901 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918965 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918965 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918965/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918965 Building REAL300004918966 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918966' /scratch/stefan/7775246/working/building/REAL300004918966 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918966 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918966/0 /scratch/stefan/7775246/working/building/REAL300004918966 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/972 `/scratch/stefan/7775246/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2=CC=C(Cl)C=C2)=NO1)C(=O)[O-]) `REAL300004918966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918966 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(Cl)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 151, 97, 97, 23, 97, 9, 1, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 151, 188, 188, 194, 194, 194, 194, 194, 151, 97, 23, 23, 9, 9, 4, 4, 4, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 978 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918966 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(Cl)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 166, 118, 118, 42, 118, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 166, 195, 195, 201, 201, 201, 201, 201, 166, 118, 42, 42, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 975 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918966 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918966 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918966/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918966 Building REAL300004918967 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918967' /scratch/stefan/7775246/working/building/REAL300004918967 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918967 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918967/0 /scratch/stefan/7775246/working/building/REAL300004918967 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/973 `/scratch/stefan/7775246/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC=C1)N1C=NN=N1)C(=O)[O-]) `REAL300004918967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918967 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)N1C=NN=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 69, 27, 27, 5, 27, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 69, 107, 107, 150, 150, 150, 150, 150, 69, 27, 5, 1, 1, 1, 1, 1, 1, 1, 23] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918967 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)N1C=NN=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 95, 45, 45, 11, 45, 1, 11, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 95, 135, 135, 177, 177, 177, 177, 177, 95, 45, 11, 23, 23, 23, 23, 23, 23, 23, 1] 201 rigid atoms, others: [39, 8, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918967 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918967 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918967/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918967 Building REAL300004918968 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918968' /scratch/stefan/7775246/working/building/REAL300004918968 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918968 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918968/0 /scratch/stefan/7775246/working/building/REAL300004918968 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/974 `/scratch/stefan/7775246/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004918968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918968 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 5, 5, 1, 5, 1, 1, 1, 1, 9, 17, 17, 13, 17, 17, 1, 1, 17, 28, 28, 40, 40, 40, 40, 40, 17, 5, 1, 9, 9, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918968 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 112, 49, 49, 17, 49, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 112, 141, 141, 201, 201, 201, 201, 201, 112, 49, 17, 4, 4, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38]) total number of confs: 905 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918968 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918968 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918968/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918968 Building REAL300004918969 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918969' /scratch/stefan/7775246/working/building/REAL300004918969 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918969 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918969/0 /scratch/stefan/7775246/working/building/REAL300004918969 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/975 `/scratch/stefan/7775246/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)N(CC)CC)C=C1)C(=O)[O-]) `REAL300004918969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918969 none CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)N(CC)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 21, 14, 14, 3, 14, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 43, 20, 47, 1, 1, 21, 25, 25, 29, 29, 29, 29, 29, 21, 14, 3, 3, 1, 1, 43, 43, 43, 43, 43, 47, 47, 47, 47, 47, 1, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 48, 49, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 425 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918969 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918969 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918969/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918969 Building REAL300004918970 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918970' /scratch/stefan/7775246/working/building/REAL300004918970 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918970 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918970/0 /scratch/stefan/7775246/working/building/REAL300004918970 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/976 `/scratch/stefan/7775246/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-]) `REAL300004918970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918970 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 42, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 13, 13, 13, 13, 42, 65, 65, 102, 102, 102, 102, 102, 42, 12, 1, 4, 4, 2, 4, 4, 13, 13, 13] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918970 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 62, 62, 13, 62, 13, 13, 13, 13, 23, 23, 13, 23, 23, 13, 1, 1, 1, 1, 1, 1, 121, 148, 148, 201, 201, 201, 201, 201, 121, 62, 13, 23, 23, 13, 23, 23, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 959 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918970 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 51, 22, 22, 4, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 23, 23, 23, 51, 76, 76, 110, 110, 110, 110, 110, 51, 22, 4, 1, 1, 1, 1, 1, 23, 23, 23] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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, 40, 41, 42]) total number of confs: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918970 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918970 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918970/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918970 Building REAL300004918971 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918971' /scratch/stefan/7775246/working/building/REAL300004918971 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918971 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918971/0 /scratch/stefan/7775246/working/building/REAL300004918971 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/977 `/scratch/stefan/7775246/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(=CC1=CC=C(F)C=C1)C1=CC=CS1)C(=O)[O-]) `REAL300004918971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918971 none CC#CCC(NC(=O)C(=CC1=CC=C(F)C=C1)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 73, 30, 30, 4, 30, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 73, 94, 94, 135, 135, 135, 135, 135, 73, 30, 4, 1, 1, 1, 1, 9, 9, 9] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918971 none CC#CCC(NC(=O)C(=CC1=CC=C(F)C=C1)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 55, 55, 7, 55, 1, 7, 7, 9, 9, 7, 7, 9, 9, 1, 1, 1, 1, 1, 115, 145, 145, 201, 201, 201, 201, 201, 115, 55, 7, 9, 9, 9, 9, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918971 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918971 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918971/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918971 Building REAL300004918972 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918972' /scratch/stefan/7775246/working/building/REAL300004918972 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918972 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918972/0 /scratch/stefan/7775246/working/building/REAL300004918972 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/978 `/scratch/stefan/7775246/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=CC=C1Cl)C(C)C)C(=O)[O-]) `REAL300004918972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918972 none CC#CCC(NC(=O)C(NC(=O)C1=CC=CC=C1Cl)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 53, 38, 38, 12, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 23, 22, 53, 55, 55, 76, 76, 76, 76, 76, 53, 38, 12, 7, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23] 82 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 382 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918972 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918972 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918972/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918972 Building REAL300004918973 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918973' /scratch/stefan/7775246/working/building/REAL300004918973 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918973 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918973/0 /scratch/stefan/7775246/working/building/REAL300004918973 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/979 `/scratch/stefan/7775246/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004918973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918973 none CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 103, 57, 57, 11, 57, 11, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 6, 6, 1, 6, 6, 103, 138, 138, 182, 182, 182, 182, 182, 103, 57, 11, 11, 1, 3, 3, 1, 3, 3, 6, 6, 1, 6, 6] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 894 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918973 none CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 87, 87, 27, 87, 27, 6, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 1, 1, 1, 1, 1, 1, 1, 135, 167, 167, 201, 201, 201, 201, 201, 135, 87, 27, 27, 6, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 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]) total number of confs: 944 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918973 none CC#CCC(NC(=O)C=CC1=CN(C2=CC=CC=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 103, 59, 59, 13, 59, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 103, 138, 138, 182, 182, 182, 182, 182, 103, 59, 13, 13, 3, 1, 1, 1, 1, 1, 7, 7, 3, 7, 7] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] 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, 45, 46, 47, 48, 49]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918973 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918973 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918973/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918973 Building REAL300004918974 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918974' /scratch/stefan/7775246/working/building/REAL300004918974 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918974 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918974/0 /scratch/stefan/7775246/working/building/REAL300004918974 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/980 `/scratch/stefan/7775246/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC(=O)C1=CSC=C1)C(=O)[O-]) `REAL300004918974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918974 none CC#CCC(NC(=O)CCCNC(=O)C1=CSC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 123, 101, 101, 35, 101, 31, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 123, 155, 155, 201, 201, 201, 201, 201, 123, 101, 34, 33, 34, 34, 21, 21, 5, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1011 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918974 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918974 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918974/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918974 Building REAL300004918975 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918975' /scratch/stefan/7775246/working/building/REAL300004918975 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918975 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918975/0 /scratch/stefan/7775246/working/building/REAL300004918975 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/981 `/scratch/stefan/7775246/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SCC1=CC=CS1)C(=O)[O-]) `REAL300004918975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918975 none CC#CCC(NC(=O)C1=CC=CC=C1SCC1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 24, 32, 32, 32, 32, 21, 31, 31, 49, 49, 49, 49, 49, 21, 8, 1, 1, 1, 1, 24, 24, 32, 32, 32] 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: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918975 none CC#CCC(NC(=O)C1=CC=CC=C1SCC1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 79, 79, 32, 79, 32, 32, 32, 32, 32, 16, 3, 1, 1, 1, 1, 1, 1, 117, 153, 153, 201, 201, 201, 201, 201, 117, 79, 32, 32, 32, 32, 3, 3, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 944 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918975 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918975 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918975/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918975 Building REAL300004918976 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918976' /scratch/stefan/7775246/working/building/REAL300004918976 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918976 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918976/0 /scratch/stefan/7775246/working/building/REAL300004918976 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/982 `/scratch/stefan/7775246/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004918976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918976 none CC#CCC(NC(=O)CCC1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 59, 22, 22, 5, 22, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 60, 84, 84, 108, 108, 108, 108, 108, 60, 22, 5, 5, 3, 3, 1, 1, 1, 1, 26, 26, 27, 27, 27] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 671 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918976 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918976 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918976/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918976 Building REAL300004918977 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918977' /scratch/stefan/7775246/working/building/REAL300004918977 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918977 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918977/0 /scratch/stefan/7775246/working/building/REAL300004918977 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/983 `/scratch/stefan/7775246/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-]) `REAL300004918977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918977 none CC#CCC(NC(=O)CCC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 60, 28, 28, 7, 28, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 60, 76, 76, 118, 118, 118, 118, 118, 60, 28, 7, 7, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 45, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918977 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918977 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918977/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918977 Building REAL300004918978 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918978' /scratch/stefan/7775246/working/building/REAL300004918978 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918978 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918978/0 /scratch/stefan/7775246/working/building/REAL300004918978 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/984 `/scratch/stefan/7775246/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC2=CC=CC=C2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004918978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918978 none CC#CCC(NC(=O)C1=CC=C(NC2=CC=CC=C2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 1, 1, 2, 2, 1, 17, 31, 31, 75, 75, 75, 75, 75, 17, 5, 1, 1, 6, 12, 12, 12, 12, 12, 1] 179 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 19, 20, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918978 none CC#CCC(NC(=O)C1=CC=C(NC2=CC=CC=C2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 118, 45, 45, 8, 45, 8, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 118, 145, 145, 179, 179, 179, 179, 179, 118, 45, 12, 12, 7, 1, 1, 1, 1, 1, 12] 179 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918978 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918978 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918978/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918978 Building REAL300004918979 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918979' /scratch/stefan/7775246/working/building/REAL300004918979 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918979 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918979/0 /scratch/stefan/7775246/working/building/REAL300004918979 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/985 `/scratch/stefan/7775246/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=CS1)C(C)C)C(=O)[O-]) `REAL300004918979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918979 none CC#CCC(NC(=O)C(NC(=O)C1=CC=CS1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 104, 62, 62, 20, 62, 7, 7, 1, 7, 1, 1, 1, 1, 1, 20, 41, 41, 104, 139, 139, 154, 154, 154, 154, 154, 104, 62, 20, 8, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 185 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 903 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918979 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918979 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918979/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918979 Building REAL300004918980 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918980' /scratch/stefan/7775246/working/building/REAL300004918980 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918980 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918980/0 /scratch/stefan/7775246/working/building/REAL300004918980 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/986 `/scratch/stefan/7775246/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-]) `REAL300004918980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918980 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 1, 1, 9, 15, 15, 39, 39, 39, 39, 39, 9, 3, 1, 1, 9, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 40, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918980 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 107, 48, 48, 28, 48, 28, 28, 28, 16, 6, 16, 16, 1, 1, 1, 1, 28, 28, 107, 139, 139, 201, 201, 201, 201, 201, 107, 48, 28, 28, 6, 1, 1, 1, 1, 1, 28, 28] 201 rigid atoms, others: [34, 35, 36, 37, 38, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 980 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918980 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918980 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918980/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918980 Building REAL300004918981 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918981' /scratch/stefan/7775246/working/building/REAL300004918981 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918981 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918981/0 /scratch/stefan/7775246/working/building/REAL300004918981 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/987 `/scratch/stefan/7775246/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CS2)=C1)C(=O)[O-]) `REAL300004918981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918981 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 19, 1, 17, 25, 25, 56, 56, 56, 56, 56, 17, 5, 1, 1, 1, 9, 19, 19, 19, 1] 201 rigid atoms, others: [32, 33, 34, 6, 39, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918981 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 106, 50, 50, 19, 50, 19, 19, 19, 19, 6, 5, 1, 5, 1, 1, 1, 1, 1, 19, 106, 141, 141, 201, 201, 201, 201, 201, 106, 50, 19, 19, 19, 6, 1, 1, 1, 19] 201 rigid atoms, others: [36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 953 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918981 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918981 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918981/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918981 Building REAL300004918982 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918982' /scratch/stefan/7775246/working/building/REAL300004918982 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918982 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918982/0 /scratch/stefan/7775246/working/building/REAL300004918982 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/988 `/scratch/stefan/7775246/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(Br)C=C2)=NN1)C(=O)[O-]) `REAL300004918982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918982 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Br)C=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 41, 12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 41, 65, 65, 107, 107, 107, 107, 107, 41, 13, 1, 7, 7, 7, 7, 1] 144 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918982 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Br)C=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 104, 55, 55, 7, 55, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 104, 122, 122, 144, 144, 144, 144, 144, 104, 55, 7, 1, 1, 1, 1, 7] 144 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918982 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918982 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918982/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918982 Building REAL300004918983 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918983' /scratch/stefan/7775246/working/building/REAL300004918983 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918983 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918983/0 /scratch/stefan/7775246/working/building/REAL300004918983 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/989 `/scratch/stefan/7775246/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(OC)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004918983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918983 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(OC)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 1, 1, 6, 4, 4, 1, 1, 1, 36, 57, 57, 100, 100, 100, 100, 100, 36, 12, 2, 2, 2, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 46, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 511 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918983 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(OC)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 64, 27, 27, 4, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 4, 64, 102, 102, 167, 167, 167, 167, 167, 64, 27, 4, 4, 4, 1, 1, 3, 3, 3, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [36, 37, 41, 42, 11, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 826 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918983 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918983 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918983/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918983 Building REAL300004918984 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918984' /scratch/stefan/7775246/working/building/REAL300004918984 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918984 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918984/0 /scratch/stefan/7775246/working/building/REAL300004918984 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/990 `/scratch/stefan/7775246/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C2=CC=CC=C12)C(=O)[O-]) `REAL300004918984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918984 none CC#CCC(NC(=O)C1=CC=C(OC)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 42, 10, 10, 1, 10, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 1, 42, 67, 67, 122, 122, 122, 122, 122, 42, 10, 1, 1, 4, 4, 4, 1, 1, 1, 1] 162 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 33, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918984 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918984 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918984/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918984 Building REAL300004918985 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918985' /scratch/stefan/7775246/working/building/REAL300004918985 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918985 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918985/0 /scratch/stefan/7775246/working/building/REAL300004918985 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/991 `/scratch/stefan/7775246/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)NC(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004918985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918985 none CC#CCC(NC(=O)CC(C)NC(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 3, 4, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 4 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918985 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918985 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918985/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918985 Building REAL300004918986 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918986' /scratch/stefan/7775246/working/building/REAL300004918986 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918986 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918986/0 /scratch/stefan/7775246/working/building/REAL300004918986 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/992 `/scratch/stefan/7775246/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCN1NC(=O)C2=CC=CC=C2C1=O)C(=O)[O-]) `REAL300004918986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918986 none CC#CCC(NC(=O)CCN1NC(=O)C2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 42, 21, 21, 5, 21, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 51, 51, 61, 61, 61, 61, 61, 42, 21, 5, 5, 3, 3, 1, 1, 1, 1, 1] 61 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918986 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918986 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918986/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918986 Building REAL300004918987 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918987' /scratch/stefan/7775246/working/building/REAL300004918987 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918987 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918987/0 /scratch/stefan/7775246/working/building/REAL300004918987 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/993 `/scratch/stefan/7775246/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(C2=CC=CC=C2)C=C1Cl)C(=O)[O-]) `REAL300004918987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918987 none CC#CCC(NC(=O)COC1=CC=C(C2=CC=CC=C2)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 149, 100, 100, 34, 100, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 149, 159, 159, 193, 193, 193, 193, 193, 149, 100, 34, 34, 1, 1, 3, 3, 1, 3, 3, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918987 none CC#CCC(NC(=O)COC1=CC=C(C2=CC=CC=C2)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 183, 142, 141, 57, 142, 14, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 183, 190, 190, 201, 201, 201, 201, 201, 183, 142, 57, 57, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42]) total number of confs: 804 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918987 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918987 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918987/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918987 Building REAL300004918988 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918988' /scratch/stefan/7775246/working/building/REAL300004918988 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918988 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918988/0 /scratch/stefan/7775246/working/building/REAL300004918988 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/994 `/scratch/stefan/7775246/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(C(C)C)C=C1)C(=O)[O-]) `REAL300004918988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918988 none CC#CCC(NC(=O)COC1=CC=C(C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 76, 46, 46, 11, 46, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 76, 85, 85, 97, 97, 97, 97, 97, 76, 46, 11, 11, 1, 1, 2, 3, 3, 3, 3, 3, 3, 1, 1] 100 rigid atoms, others: [32, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 454 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918988 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918988 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918988/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918988 Building REAL300004918989 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918989' /scratch/stefan/7775246/working/building/REAL300004918989 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918989 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918989/0 /scratch/stefan/7775246/working/building/REAL300004918989 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/995 `/scratch/stefan/7775246/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OC)C(=O)[O-]) `REAL300004918989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918989 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 47, 13, 13, 1, 13, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 3, 47, 72, 72, 133, 133, 133, 133, 133, 47, 13, 4, 4, 1, 4, 4, 1, 4, 4, 4] 185 rigid atoms, others: [36, 6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918989 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 74, 30, 30, 4, 30, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 74, 107, 107, 158, 158, 158, 158, 158, 74, 30, 1, 1, 1, 1, 1, 4, 10, 10, 10] 185 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918989 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918989 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918989/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918989 Building REAL300004918990 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918990' /scratch/stefan/7775246/working/building/REAL300004918990 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918990 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918990/0 /scratch/stefan/7775246/working/building/REAL300004918990 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/996 `/scratch/stefan/7775246/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(C)=O)C=C1)C(=O)[O-]) `REAL300004918990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918990 none CC#CCC(NC(=O)C1=CC=C(CNC(C)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 37, 37, 37, 1, 1, 9, 13, 13, 29, 29, 29, 29, 29, 9, 3, 1, 1, 6, 6, 37, 38, 38, 38, 1, 1] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 17, 18, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918990 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918990 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918990/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918990 Building REAL300004918991 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918991' /scratch/stefan/7775246/working/building/REAL300004918991 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918991 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918991/0 /scratch/stefan/7775246/working/building/REAL300004918991 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/997 `/scratch/stefan/7775246/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(NC(C)=O)C=C1)C(=O)[O-]) `REAL300004918991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918991 none CC#CCC(NC(=O)CC1=CC=C(NC(C)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 33, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 33, 55, 55, 104, 104, 104, 104, 104, 33, 9, 4, 4, 1, 1, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918991 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918991 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918991/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918991 Building REAL300004918992 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918992' /scratch/stefan/7775246/working/building/REAL300004918992 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918992 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918992/0 /scratch/stefan/7775246/working/building/REAL300004918992 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/998 `/scratch/stefan/7775246/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2CC2)=C1)C(=O)[O-]) `REAL300004918992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918992 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 6, 6, 6, 16, 33, 33, 1, 17, 25, 25, 48, 48, 48, 48, 48, 17, 5, 1, 1, 3, 3, 3, 16, 33, 33, 33, 33, 33, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 14, 15, 22, 44] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918992 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 137, 81, 81, 33, 81, 33, 33, 33, 33, 33, 35, 19, 6, 19, 19, 1, 1, 1, 1, 33, 137, 152, 152, 201, 201, 201, 201, 201, 137, 81, 33, 33, 35, 35, 35, 6, 1, 1, 1, 1, 1, 33] 201 rigid atoms, others: [39, 40, 41, 42, 43, 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, 35, 36, 37, 38, 44]) total number of confs: 889 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918992 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918992 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918992/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918992 Building REAL300004918993 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918993' /scratch/stefan/7775246/working/building/REAL300004918993 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918993 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918993/0 /scratch/stefan/7775246/working/building/REAL300004918993 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/999 `/scratch/stefan/7775246/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1C(C)(C)C)C(=O)[O-]) `REAL300004918993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918993 none CC#CCC(NC(=O)COC1=CC=CC=C1C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 85, 85, 18, 84, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 128, 164, 164, 201, 201, 201, 201, 201, 128, 85, 18, 18, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 955 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918993 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918993 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918993/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918993 Building REAL300004918994 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918994' /scratch/stefan/7775246/working/building/REAL300004918994 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918994 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918994/0 /scratch/stefan/7775246/working/building/REAL300004918994 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1000 `/scratch/stefan/7775246/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-]) `REAL300004918994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918994 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 43, 12, 12, 1, 12, 1, 1, 1, 4, 4, 1, 1, 6, 6, 2, 3, 6, 6, 1, 1, 43, 59, 59, 101, 101, 101, 101, 101, 43, 12, 4, 4, 4, 4, 4, 6, 6, 6, 6] 115 rigid atoms, others: [6, 8, 9, 10, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918994 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 69, 25, 25, 6, 25, 6, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 69, 88, 88, 115, 115, 115, 115, 115, 69, 25, 7, 7, 7, 7, 7, 1, 1, 1, 1] 115 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918994 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=C(F)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 61, 20, 20, 4, 20, 4, 1, 1, 1, 1, 4, 4, 7, 7, 4, 5, 7, 7, 4, 4, 61, 81, 81, 114, 114, 114, 114, 114, 61, 20, 1, 1, 1, 1, 1, 7, 7, 7, 7] 115 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918994 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918994 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918994/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918994 Building REAL300004918995 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918995' /scratch/stefan/7775246/working/building/REAL300004918995 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918995 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918995/0 /scratch/stefan/7775246/working/building/REAL300004918995 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1001 `/scratch/stefan/7775246/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-]) `REAL300004918995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.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: REAL300004918995 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 47, 12, 12, 1, 12, 1, 1, 1, 4, 4, 1, 1, 6, 6, 1, 6, 6, 1, 1, 47, 65, 65, 109, 109, 109, 109, 109, 47, 12, 4, 4, 4, 4, 4, 6, 6, 1, 6, 6] 127 rigid atoms, others: [6, 8, 9, 10, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918995 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 73, 25, 25, 6, 25, 6, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 73, 90, 90, 127, 127, 127, 127, 127, 73, 25, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 127 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918995 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 69, 22, 22, 4, 22, 4, 1, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 4, 4, 69, 86, 86, 126, 126, 126, 126, 126, 69, 22, 1, 1, 1, 1, 1, 7, 7, 5, 7, 7] 127 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918995 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918995 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918995/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918995 Building REAL300004918996 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918996' /scratch/stefan/7775246/working/building/REAL300004918996 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918996 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918996/0 /scratch/stefan/7775246/working/building/REAL300004918996 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1002 `/scratch/stefan/7775246/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=C(F)C=C2)C1)C(=O)[O-]) `REAL300004918996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.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: REAL300004918996 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=C(F)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 8, 7, 19, 19, 1, 21, 34, 34, 51, 51, 51, 51, 51, 21, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004918996 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=C(F)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 85, 85, 19, 85, 19, 19, 19, 19, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 19, 139, 175, 175, 201, 201, 201, 201, 201, 139, 85, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [41, 42, 43, 44, 13, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918996 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918996 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918996/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918996 Building REAL300004918997 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918997' /scratch/stefan/7775246/working/building/REAL300004918997 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918997 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918997/0 /scratch/stefan/7775246/working/building/REAL300004918997 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1003 `/scratch/stefan/7775246/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)C1=C(C=CC=C1)S2)C(=O)[O-]) `REAL300004918997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918997 none CC#CCC(NC(=O)C1=CC2=C(S1)C1=C(C=CC=C1)S2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 42, 42, 63, 63, 63, 63, 63, 32, 11, 1, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918997 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918997 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918997/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918997 Building REAL300004918998 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918998' /scratch/stefan/7775246/working/building/REAL300004918998 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918998 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918998/0 /scratch/stefan/7775246/working/building/REAL300004918998 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1004 `/scratch/stefan/7775246/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1C2=CC=CC=C2C=CN1C(C)=O)C(=O)[O-]) `REAL300004918998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918998 none CC#CCC(NC(=O)CC1C2=CC=CC=C2C=CN1C(C)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 15, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 16, 16, 24, 24, 24, 24, 24, 15, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918998 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918998 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918998/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918998 Building REAL300004918999 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004918999' /scratch/stefan/7775246/working/building/REAL300004918999 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004918999 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004918999/0 /scratch/stefan/7775246/working/building/REAL300004918999 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1005 `/scratch/stefan/7775246/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C(=O)COC2=CC=C([N+](=O)[O-])C=C21)C(=O)[O-]) `REAL300004918999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004918999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004918999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004918999 none CC#CCC(NC(=O)CN1C(=O)COC2=CC=C([N+](=O)[O-])C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 98, 38, 38, 7, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 138, 138, 200, 200, 200, 200, 200, 98, 38, 7, 7, 1, 1, 1, 1, 1] 200 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 981 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004918999 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004918999 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004918999/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004918999 Building REAL300004919000 mkdir: created directory `/scratch/stefan/7775246/working/building/REAL300004919000' /scratch/stefan/7775246/working/building/REAL300004919000 /scratch/stefan/7775246/working /scratch/stefan/7775246 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919000 mkdir: created directory `0' /scratch/stefan/7775246/working/building/REAL300004919000/0 /scratch/stefan/7775246/working/building/REAL300004919000 /scratch/stefan/7775246/working /scratch/stefan/7775246 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7775246/working/3D/1006 `/scratch/stefan/7775246/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(C(C)=O)C=C1OC)C(=O)[O-]) `REAL300004919000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775246/working/building/REAL300004919000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004919000 none CC#CCC(NC(=O)CCCOC1=CC=C(C(C)=O)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 134, 119, 119, 58, 119, 45, 26, 10, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 3, 134, 134, 134, 155, 155, 155, 155, 155, 134, 119, 58, 58, 49, 49, 26, 26, 1, 1, 8, 8, 8, 1, 4, 4, 4] 201 rigid atoms, others: [39, 40, 44, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 45, 46, 47]) total number of confs: 704 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775246/working/building/REAL300004919000 /scratch/stefan/7775246/working /scratch/stefan/7775246 Finished preparing REAL300004919000 Recording results /scratch/stefan/7775246/working /scratch/stefan/7775246 Appending to /scratch/stefan/7775246/finished/xaaabji.* 0: /scratch/stefan/7775246/working/building/REAL300004919000/0.* Removing working files in /scratch/stefan/7775246/working/building/REAL300004919000 /scratch/stefan/7775246 Compressing combined databse files /scratch/stefan/7775246/finished/xaaabji.db2.gz /scratch/stefan/7775246/finished/xaaabji.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7775246/finished) ======================================================= Finalizing... removed `/scratch/stefan/7775246/working/3D/1007' removed directory: `/scratch/stefan/7775246/working/3D' `/scratch/stefan/7775246/working/protonate' -> `/scratch/stefan/7775246/archive' `/scratch/stefan/7775246/working/input-smiles.ism' -> `/scratch/stefan/7775246/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7775246/working/building' rmdir: removing directory, `/scratch/stefan/7775246/working' ls: No match. ls: No match.